HEADER TRANSPORT PROTEIN 03-AUG-25 9W65 TITLE CRYO-EM STRUCTURE OF ATP BOUND STATE HUMAN ABCD3 IN INWARD-FACING TITLE 2 CONFORMATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-BINDING CASSETTE SUB-FAMILY D MEMBER 3,GREEN COMPND 3 FLUORESCENT PROTEIN; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: 70 KDA PEROXISOMAL MEMBRANE PROTEIN,PMP70; COMPND 6 EC: 3.1.2.-,7.6.2.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ABCD3, PMP70, PXMP1, GFP; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS ABC TRANSPORTER, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR S.AIBA,H.H.OKAMOTO,K.F.SANO,T.KUSAKIZAKO,O.NUREKI REVDAT 1 27-MAY-26 9W65 0 JRNL AUTH S.AIBA,H.H.OKAMOTO,A.TOMITA,F.SANO,T.KUSAKIZAKO,O.NUREKI JRNL TITL STRUCTURAL INSIGHTS INTO THE BROAD SUBSTRATE RECOGNITION JRNL TITL 2 MECHANISM OF HUMAN ABCD3 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 2.940 REMARK 3 NUMBER OF PARTICLES : 65336 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9W65 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-AUG-25. REMARK 100 THE DEPOSITION ID IS D_1300062301. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : ATP BOUND ABCD3 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1600.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 332.00012 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 332.00012 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 ALA A 3 REMARK 465 PHE A 4 REMARK 465 SER A 5 REMARK 465 LYS A 6 REMARK 465 TYR A 7 REMARK 465 LEU A 8 REMARK 465 THR A 9 REMARK 465 ALA A 10 REMARK 465 ARG A 11 REMARK 465 ASN A 12 REMARK 465 SER A 13 REMARK 465 SER A 14 REMARK 465 LEU A 15 REMARK 465 ALA A 16 REMARK 465 GLY A 17 REMARK 465 ALA A 18 REMARK 465 ALA A 19 REMARK 465 PHE A 20 REMARK 465 LEU A 21 REMARK 465 LEU A 22 REMARK 465 LEU A 23 REMARK 465 CYS A 24 REMARK 465 LEU A 25 REMARK 465 LEU A 26 REMARK 465 HIS A 27 REMARK 465 LYS A 28 REMARK 465 ARG A 29 REMARK 465 ARG A 30 REMARK 465 ARG A 31 REMARK 465 ALA A 32 REMARK 465 LEU A 33 REMARK 465 GLY A 34 REMARK 465 LEU A 35 REMARK 465 HIS A 36 REMARK 465 GLY A 37 REMARK 465 LYS A 38 REMARK 465 LYS A 39 REMARK 465 SER A 40 REMARK 465 GLY A 41 REMARK 465 LYS A 42 REMARK 465 PRO A 43 REMARK 465 PRO A 44 REMARK 465 LEU A 45 REMARK 465 GLN A 46 REMARK 465 ASN A 47 REMARK 465 ASN A 48 REMARK 465 GLU A 49 REMARK 465 LYS A 50 REMARK 465 GLU A 51 REMARK 465 GLY A 52 REMARK 465 LYS A 53 REMARK 465 LYS A 54 REMARK 465 GLU A 55 REMARK 465 ARG A 56 REMARK 465 ALA A 57 REMARK 465 VAL A 411 REMARK 465 SER A 412 REMARK 465 GLN A 413 REMARK 465 GLN A 414 REMARK 465 GLU A 415 REMARK 465 LYS A 416 REMARK 465 GLY A 417 REMARK 465 ILE A 418 REMARK 465 GLU A 419 REMARK 465 GLY A 420 REMARK 465 VAL A 421 REMARK 465 GLN A 422 REMARK 465 VAL A 423 REMARK 465 ILE A 424 REMARK 465 PRO A 425 REMARK 465 LEU A 426 REMARK 465 ILE A 427 REMARK 465 PRO A 428 REMARK 465 GLY A 429 REMARK 465 GLU A 652 REMARK 465 ASP A 653 REMARK 465 THR A 654 REMARK 465 VAL A 655 REMARK 465 GLU A 656 REMARK 465 PHE A 657 REMARK 465 GLY A 658 REMARK 465 SER A 659 REMARK 465 LEU A 660 REMARK 465 GLU A 661 REMARK 465 VAL A 662 REMARK 465 LEU A 663 REMARK 465 PHE A 664 REMARK 465 GLN A 665 REMARK 465 GLY A 666 REMARK 465 PRO A 667 REMARK 465 ALA A 668 REMARK 465 VAL A 669 REMARK 465 SER A 670 REMARK 465 LYS A 671 REMARK 465 GLY A 672 REMARK 465 GLU A 673 REMARK 465 GLU A 674 REMARK 465 LEU A 675 REMARK 465 PHE A 676 REMARK 465 THR A 677 REMARK 465 GLY A 678 REMARK 465 VAL A 679 REMARK 465 VAL A 680 REMARK 465 PRO A 681 REMARK 465 ILE A 682 REMARK 465 LEU A 683 REMARK 465 VAL A 684 REMARK 465 GLU A 685 REMARK 465 LEU A 686 REMARK 465 ASP A 687 REMARK 465 GLY A 688 REMARK 465 ASP A 689 REMARK 465 VAL A 690 REMARK 465 ASN A 691 REMARK 465 GLY A 692 REMARK 465 HIS A 693 REMARK 465 LYS A 694 REMARK 465 PHE A 695 REMARK 465 SER A 696 REMARK 465 VAL A 697 REMARK 465 SER A 698 REMARK 465 GLY A 699 REMARK 465 GLU A 700 REMARK 465 GLY A 701 REMARK 465 GLU A 702 REMARK 465 GLY A 703 REMARK 465 ASP A 704 REMARK 465 ALA A 705 REMARK 465 THR A 706 REMARK 465 TYR A 707 REMARK 465 GLY A 708 REMARK 465 LYS A 709 REMARK 465 LEU A 710 REMARK 465 THR A 711 REMARK 465 LEU A 712 REMARK 465 LYS A 713 REMARK 465 PHE A 714 REMARK 465 ILE A 715 REMARK 465 CYS A 716 REMARK 465 THR A 717 REMARK 465 THR A 718 REMARK 465 GLY A 719 REMARK 465 LYS A 720 REMARK 465 LEU A 721 REMARK 465 PRO A 722 REMARK 465 VAL A 723 REMARK 465 PRO A 724 REMARK 465 TRP A 725 REMARK 465 PRO A 726 REMARK 465 THR A 727 REMARK 465 LEU A 728 REMARK 465 VAL A 729 REMARK 465 THR A 730 REMARK 465 THR A 731 REMARK 465 LEU A 732 REMARK 465 THR A 733 REMARK 465 TYR A 734 REMARK 465 GLY A 735 REMARK 465 VAL A 736 REMARK 465 GLN A 737 REMARK 465 CYS A 738 REMARK 465 PHE A 739 REMARK 465 SER A 740 REMARK 465 ARG A 741 REMARK 465 TYR A 742 REMARK 465 PRO A 743 REMARK 465 ASP A 744 REMARK 465 HIS A 745 REMARK 465 MET A 746 REMARK 465 LYS A 747 REMARK 465 GLN A 748 REMARK 465 HIS A 749 REMARK 465 ASP A 750 REMARK 465 PHE A 751 REMARK 465 PHE A 752 REMARK 465 LYS A 753 REMARK 465 SER A 754 REMARK 465 ALA A 755 REMARK 465 MET A 756 REMARK 465 PRO A 757 REMARK 465 GLU A 758 REMARK 465 GLY A 759 REMARK 465 TYR A 760 REMARK 465 VAL A 761 REMARK 465 GLN A 762 REMARK 465 GLU A 763 REMARK 465 ARG A 764 REMARK 465 THR A 765 REMARK 465 ILE A 766 REMARK 465 PHE A 767 REMARK 465 PHE A 768 REMARK 465 LYS A 769 REMARK 465 ASP A 770 REMARK 465 ASP A 771 REMARK 465 GLY A 772 REMARK 465 ASN A 773 REMARK 465 TYR A 774 REMARK 465 LYS A 775 REMARK 465 THR A 776 REMARK 465 ARG A 777 REMARK 465 ALA A 778 REMARK 465 GLU A 779 REMARK 465 VAL A 780 REMARK 465 LYS A 781 REMARK 465 PHE A 782 REMARK 465 GLU A 783 REMARK 465 GLY A 784 REMARK 465 ASP A 785 REMARK 465 THR A 786 REMARK 465 LEU A 787 REMARK 465 VAL A 788 REMARK 465 ASN A 789 REMARK 465 ARG A 790 REMARK 465 ILE A 791 REMARK 465 GLU A 792 REMARK 465 LEU A 793 REMARK 465 LYS A 794 REMARK 465 GLY A 795 REMARK 465 ILE A 796 REMARK 465 ASP A 797 REMARK 465 PHE A 798 REMARK 465 LYS A 799 REMARK 465 GLU A 800 REMARK 465 ASP A 801 REMARK 465 GLY A 802 REMARK 465 ASN A 803 REMARK 465 ILE A 804 REMARK 465 LEU A 805 REMARK 465 GLY A 806 REMARK 465 HIS A 807 REMARK 465 LYS A 808 REMARK 465 LEU A 809 REMARK 465 GLU A 810 REMARK 465 TYR A 811 REMARK 465 ASN A 812 REMARK 465 TYR A 813 REMARK 465 ASN A 814 REMARK 465 SER A 815 REMARK 465 HIS A 816 REMARK 465 ASN A 817 REMARK 465 VAL A 818 REMARK 465 TYR A 819 REMARK 465 ILE A 820 REMARK 465 MET A 821 REMARK 465 ALA A 822 REMARK 465 ASP A 823 REMARK 465 LYS A 824 REMARK 465 GLN A 825 REMARK 465 LYS A 826 REMARK 465 ASN A 827 REMARK 465 GLY A 828 REMARK 465 ILE A 829 REMARK 465 LYS A 830 REMARK 465 VAL A 831 REMARK 465 ASN A 832 REMARK 465 PHE A 833 REMARK 465 LYS A 834 REMARK 465 ILE A 835 REMARK 465 ARG A 836 REMARK 465 HIS A 837 REMARK 465 ASN A 838 REMARK 465 ILE A 839 REMARK 465 GLU A 840 REMARK 465 ASP A 841 REMARK 465 GLY A 842 REMARK 465 SER A 843 REMARK 465 VAL A 844 REMARK 465 GLN A 845 REMARK 465 LEU A 846 REMARK 465 ALA A 847 REMARK 465 ASP A 848 REMARK 465 HIS A 849 REMARK 465 TYR A 850 REMARK 465 GLN A 851 REMARK 465 GLN A 852 REMARK 465 ASN A 853 REMARK 465 THR A 854 REMARK 465 PRO A 855 REMARK 465 ILE A 856 REMARK 465 GLY A 857 REMARK 465 ASP A 858 REMARK 465 GLY A 859 REMARK 465 PRO A 860 REMARK 465 VAL A 861 REMARK 465 LEU A 862 REMARK 465 LEU A 863 REMARK 465 PRO A 864 REMARK 465 ASP A 865 REMARK 465 ASN A 866 REMARK 465 HIS A 867 REMARK 465 TYR A 868 REMARK 465 LEU A 869 REMARK 465 SER A 870 REMARK 465 THR A 871 REMARK 465 GLN A 872 REMARK 465 SER A 873 REMARK 465 LYS A 874 REMARK 465 LEU A 875 REMARK 465 SER A 876 REMARK 465 LYS A 877 REMARK 465 ASP A 878 REMARK 465 PRO A 879 REMARK 465 ASN A 880 REMARK 465 GLU A 881 REMARK 465 LYS A 882 REMARK 465 ARG A 883 REMARK 465 ASP A 884 REMARK 465 HIS A 885 REMARK 465 MET A 886 REMARK 465 VAL A 887 REMARK 465 LEU A 888 REMARK 465 LEU A 889 REMARK 465 GLU A 890 REMARK 465 PHE A 891 REMARK 465 VAL A 892 REMARK 465 THR A 893 REMARK 465 ALA A 894 REMARK 465 ALA A 895 REMARK 465 GLY A 896 REMARK 465 ILE A 897 REMARK 465 THR A 898 REMARK 465 LEU A 899 REMARK 465 GLY A 900 REMARK 465 MET A 901 REMARK 465 ASP A 902 REMARK 465 GLU A 903 REMARK 465 LEU A 904 REMARK 465 TYR A 905 REMARK 465 LYS A 906 REMARK 465 HIS A 907 REMARK 465 HIS A 908 REMARK 465 HIS A 909 REMARK 465 HIS A 910 REMARK 465 HIS A 911 REMARK 465 HIS A 912 REMARK 465 HIS A 913 REMARK 465 HIS A 914 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 TYR A 261 CB - CG - CD1 ANGL. DEV. = 3.9 DEGREES REMARK 500 PHE A 306 CB - CG - CD1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 335 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 373 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 PHE A 493 CB - CG - CD1 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG A 614 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 112 -37.61 -38.19 REMARK 500 ARG A 117 42.60 70.20 REMARK 500 PHE A 170 4.46 92.40 REMARK 500 LEU A 178 -63.53 -107.36 REMARK 500 THR A 190 -66.12 -120.12 REMARK 500 LEU A 340 -23.88 83.38 REMARK 500 ALA A 436 -150.48 49.42 REMARK 500 THR A 449 146.54 -37.27 REMARK 500 SER A 465 143.99 -37.27 REMARK 500 ASN A 468 74.96 40.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ILE A 524 TYR A 525 -143.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1004 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 480 OG REMARK 620 2 GLN A 510 OE1 128.4 REMARK 620 3 ATP A1003 O3G 143.6 84.5 REMARK 620 4 ATP A1003 O2B 70.6 160.9 77.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1002 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP A1001 O2G REMARK 620 2 ATP A1001 O1B 76.1 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-65677 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF ATP BOUND STATE HUMAN ABCD3 IN INWARD-FACING REMARK 900 CONFORMATION DBREF 9W65 A 1 659 UNP P28288 ABCD3_HUMAN 1 659 DBREF 9W65 A 669 906 UNP P42212 GFP_AEQVI 1 238 SEQADV 9W65 GLN A 596 UNP P28288 GLU 596 ENGINEERED MUTATION SEQADV 9W65 LEU A 660 UNP P28288 LINKER SEQADV 9W65 GLU A 661 UNP P28288 LINKER SEQADV 9W65 VAL A 662 UNP P28288 LINKER SEQADV 9W65 LEU A 663 UNP P28288 LINKER SEQADV 9W65 PHE A 664 UNP P28288 LINKER SEQADV 9W65 GLN A 665 UNP P28288 LINKER SEQADV 9W65 GLY A 666 UNP P28288 LINKER SEQADV 9W65 PRO A 667 UNP P28288 LINKER SEQADV 9W65 ALA A 668 UNP P28288 LINKER SEQADV 9W65 VAL A 669 UNP P42212 MET 1 CONFLICT SEQADV 9W65 LEU A 732 UNP P42212 PHE 64 CONFLICT SEQADV 9W65 THR A 733 UNP P42212 SER 65 CONFLICT SEQADV 9W65 LYS A 874 UNP P42212 ALA 206 CONFLICT SEQADV 9W65 LEU A 899 UNP P42212 HIS 231 CONFLICT SEQADV 9W65 HIS A 907 UNP P42212 EXPRESSION TAG SEQADV 9W65 HIS A 908 UNP P42212 EXPRESSION TAG SEQADV 9W65 HIS A 909 UNP P42212 EXPRESSION TAG SEQADV 9W65 HIS A 910 UNP P42212 EXPRESSION TAG SEQADV 9W65 HIS A 911 UNP P42212 EXPRESSION TAG SEQADV 9W65 HIS A 912 UNP P42212 EXPRESSION TAG SEQADV 9W65 HIS A 913 UNP P42212 EXPRESSION TAG SEQADV 9W65 HIS A 914 UNP P42212 EXPRESSION TAG SEQRES 1 A 914 MET ALA ALA PHE SER LYS TYR LEU THR ALA ARG ASN SER SEQRES 2 A 914 SER LEU ALA GLY ALA ALA PHE LEU LEU LEU CYS LEU LEU SEQRES 3 A 914 HIS LYS ARG ARG ARG ALA LEU GLY LEU HIS GLY LYS LYS SEQRES 4 A 914 SER GLY LYS PRO PRO LEU GLN ASN ASN GLU LYS GLU GLY SEQRES 5 A 914 LYS LYS GLU ARG ALA VAL VAL ASP LYS VAL PHE PHE SER SEQRES 6 A 914 ARG LEU ILE GLN ILE LEU LYS ILE MET VAL PRO ARG THR SEQRES 7 A 914 PHE CYS LYS GLU THR GLY TYR LEU VAL LEU ILE ALA VAL SEQRES 8 A 914 MET LEU VAL SER ARG THR TYR CYS ASP VAL TRP MET ILE SEQRES 9 A 914 GLN ASN GLY THR LEU ILE GLU SER GLY ILE ILE GLY ARG SEQRES 10 A 914 SER ARG LYS ASP PHE LYS ARG TYR LEU LEU ASN PHE ILE SEQRES 11 A 914 ALA ALA MET PRO LEU ILE SER LEU VAL ASN ASN PHE LEU SEQRES 12 A 914 LYS TYR GLY LEU ASN GLU LEU LYS LEU CYS PHE ARG VAL SEQRES 13 A 914 ARG LEU THR LYS TYR LEU TYR GLU GLU TYR LEU GLN ALA SEQRES 14 A 914 PHE THR TYR TYR LYS MET GLY ASN LEU ASP ASN ARG ILE SEQRES 15 A 914 ALA ASN PRO ASP GLN LEU LEU THR GLN ASP VAL GLU LYS SEQRES 16 A 914 PHE CYS ASN SER VAL VAL ASP LEU TYR SER ASN LEU SER SEQRES 17 A 914 LYS PRO PHE LEU ASP ILE VAL LEU TYR ILE PHE LYS LEU SEQRES 18 A 914 THR SER ALA ILE GLY ALA GLN GLY PRO ALA SER MET MET SEQRES 19 A 914 ALA TYR LEU VAL VAL SER GLY LEU PHE LEU THR ARG LEU SEQRES 20 A 914 ARG ARG PRO ILE GLY LYS MET THR ILE THR GLU GLN LYS SEQRES 21 A 914 TYR GLU GLY GLU TYR ARG TYR VAL ASN SER ARG LEU ILE SEQRES 22 A 914 THR ASN SER GLU GLU ILE ALA PHE TYR ASN GLY ASN LYS SEQRES 23 A 914 ARG GLU LYS GLN THR VAL HIS SER VAL PHE ARG LYS LEU SEQRES 24 A 914 VAL GLU HIS LEU HIS ASN PHE ILE LEU PHE ARG PHE SER SEQRES 25 A 914 MET GLY PHE ILE ASP SER ILE ILE ALA LYS TYR LEU ALA SEQRES 26 A 914 THR VAL VAL GLY TYR LEU VAL VAL SER ARG PRO PHE LEU SEQRES 27 A 914 ASP LEU SER HIS PRO ARG HIS LEU LYS SER THR HIS SER SEQRES 28 A 914 GLU LEU LEU GLU ASP TYR TYR GLN SER GLY ARG MET LEU SEQRES 29 A 914 LEU ARG MET SER GLN ALA LEU GLY ARG ILE VAL LEU ALA SEQRES 30 A 914 GLY ARG GLU MET THR ARG LEU ALA GLY PHE THR ALA ARG SEQRES 31 A 914 ILE THR GLU LEU MET GLN VAL LEU LYS ASP LEU ASN HIS SEQRES 32 A 914 GLY LYS TYR GLU ARG THR MET VAL SER GLN GLN GLU LYS SEQRES 33 A 914 GLY ILE GLU GLY VAL GLN VAL ILE PRO LEU ILE PRO GLY SEQRES 34 A 914 ALA GLY GLU ILE ILE ILE ALA ASP ASN ILE ILE LYS PHE SEQRES 35 A 914 ASP HIS VAL PRO LEU ALA THR PRO ASN GLY ASP VAL LEU SEQRES 36 A 914 ILE ARG ASP LEU ASN PHE GLU VAL ARG SER GLY ALA ASN SEQRES 37 A 914 VAL LEU ILE CYS GLY PRO ASN GLY CYS GLY LYS SER SER SEQRES 38 A 914 LEU PHE ARG VAL LEU GLY GLU LEU TRP PRO LEU PHE GLY SEQRES 39 A 914 GLY ARG LEU THR LYS PRO GLU ARG GLY LYS LEU PHE TYR SEQRES 40 A 914 VAL PRO GLN ARG PRO TYR MET THR LEU GLY THR LEU ARG SEQRES 41 A 914 ASP GLN VAL ILE TYR PRO ASP GLY ARG GLU ASP GLN LYS SEQRES 42 A 914 ARG LYS GLY ILE SER ASP LEU VAL LEU LYS GLU TYR LEU SEQRES 43 A 914 ASP ASN VAL GLN LEU GLY HIS ILE LEU GLU ARG GLU GLY SEQRES 44 A 914 GLY TRP ASP SER VAL GLN ASP TRP MET ASP VAL LEU SER SEQRES 45 A 914 GLY GLY GLU LYS GLN ARG MET ALA MET ALA ARG LEU PHE SEQRES 46 A 914 TYR HIS LYS PRO GLN PHE ALA ILE LEU ASP GLN CYS THR SEQRES 47 A 914 SER ALA VAL SER VAL ASP VAL GLU GLY TYR ILE TYR SER SEQRES 48 A 914 HIS CYS ARG LYS VAL GLY ILE THR LEU PHE THR VAL SER SEQRES 49 A 914 HIS ARG LYS SER LEU TRP LYS HIS HIS GLU TYR TYR LEU SEQRES 50 A 914 HIS MET ASP GLY ARG GLY ASN TYR GLU PHE LYS GLN ILE SEQRES 51 A 914 THR GLU ASP THR VAL GLU PHE GLY SER LEU GLU VAL LEU SEQRES 52 A 914 PHE GLN GLY PRO ALA VAL SER LYS GLY GLU GLU LEU PHE SEQRES 53 A 914 THR GLY VAL VAL PRO ILE LEU VAL GLU LEU ASP GLY ASP SEQRES 54 A 914 VAL ASN GLY HIS LYS PHE SER VAL SER GLY GLU GLY GLU SEQRES 55 A 914 GLY ASP ALA THR TYR GLY LYS LEU THR LEU LYS PHE ILE SEQRES 56 A 914 CYS THR THR GLY LYS LEU PRO VAL PRO TRP PRO THR LEU SEQRES 57 A 914 VAL THR THR LEU THR TYR GLY VAL GLN CYS PHE SER ARG SEQRES 58 A 914 TYR PRO ASP HIS MET LYS GLN HIS ASP PHE PHE LYS SER SEQRES 59 A 914 ALA MET PRO GLU GLY TYR VAL GLN GLU ARG THR ILE PHE SEQRES 60 A 914 PHE LYS ASP ASP GLY ASN TYR LYS THR ARG ALA GLU VAL SEQRES 61 A 914 LYS PHE GLU GLY ASP THR LEU VAL ASN ARG ILE GLU LEU SEQRES 62 A 914 LYS GLY ILE ASP PHE LYS GLU ASP GLY ASN ILE LEU GLY SEQRES 63 A 914 HIS LYS LEU GLU TYR ASN TYR ASN SER HIS ASN VAL TYR SEQRES 64 A 914 ILE MET ALA ASP LYS GLN LYS ASN GLY ILE LYS VAL ASN SEQRES 65 A 914 PHE LYS ILE ARG HIS ASN ILE GLU ASP GLY SER VAL GLN SEQRES 66 A 914 LEU ALA ASP HIS TYR GLN GLN ASN THR PRO ILE GLY ASP SEQRES 67 A 914 GLY PRO VAL LEU LEU PRO ASP ASN HIS TYR LEU SER THR SEQRES 68 A 914 GLN SER LYS LEU SER LYS ASP PRO ASN GLU LYS ARG ASP SEQRES 69 A 914 HIS MET VAL LEU LEU GLU PHE VAL THR ALA ALA GLY ILE SEQRES 70 A 914 THR LEU GLY MET ASP GLU LEU TYR LYS HIS HIS HIS HIS SEQRES 71 A 914 HIS HIS HIS HIS HET ATP A1001 31 HET MG A1002 1 HET ATP A1003 31 HET MG A1004 1 HET CLR A1005 28 HET CLR A1006 28 HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM CLR CHOLESTEROL FORMUL 2 ATP 2(C10 H16 N5 O13 P3) FORMUL 3 MG 2(MG 2+) FORMUL 6 CLR 2(C27 H46 O) HELIX 1 AA1 ASP A 60 VAL A 75 1 16 HELIX 2 AA2 CYS A 80 GLY A 116 1 37 HELIX 3 AA3 SER A 118 LEU A 167 1 50 HELIX 4 AA4 PHE A 170 LEU A 178 1 9 HELIX 5 AA5 ASN A 184 ILE A 225 1 42 HELIX 6 AA6 ALA A 227 ARG A 248 1 22 HELIX 7 AA7 ARG A 248 ASN A 275 1 28 HELIX 8 AA8 ASN A 275 ASN A 283 1 9 HELIX 9 AA9 GLY A 284 LYS A 322 1 39 HELIX 10 AB1 LYS A 322 LEU A 340 1 19 HELIX 11 AB2 THR A 349 ASN A 402 1 54 HELIX 12 AB3 GLY A 478 GLY A 487 1 10 HELIX 13 AB4 GLU A 501 GLY A 503 5 3 HELIX 14 AB5 THR A 518 ILE A 524 1 7 HELIX 15 AB6 GLY A 528 GLY A 536 1 9 HELIX 16 AB7 SER A 538 VAL A 549 1 12 HELIX 17 AB8 LEU A 551 GLU A 558 1 8 HELIX 18 AB9 ASP A 566 LEU A 571 1 6 HELIX 19 AC1 SER A 572 LYS A 588 1 17 HELIX 20 AC2 SER A 602 GLY A 617 1 16 HELIX 21 AC3 ARG A 626 LYS A 631 1 6 SHEET 1 AA1 4 GLU A 432 ILE A 434 0 SHEET 2 AA1 4 ARG A 496 THR A 498 1 O LEU A 497 N GLU A 432 SHEET 3 AA1 4 ILE A 440 ASP A 443 -1 N ASP A 443 O ARG A 496 SHEET 4 AA1 4 PHE A 461 VAL A 463 -1 O PHE A 461 N PHE A 442 SHEET 1 AA2 2 LEU A 447 ALA A 448 0 SHEET 2 AA2 2 VAL A 454 ILE A 456 -1 O LEU A 455 N LEU A 447 SHEET 1 AA3 3 LEU A 470 CYS A 472 0 SHEET 2 AA3 3 TYR A 635 MET A 639 1 O MET A 639 N CYS A 472 SHEET 3 AA3 3 TYR A 645 GLN A 649 -1 O GLU A 646 N HIS A 638 SHEET 1 AA4 3 LEU A 505 VAL A 508 0 SHEET 2 AA4 3 PHE A 591 ASP A 595 1 O ILE A 593 N VAL A 508 SHEET 3 AA4 3 THR A 619 VAL A 623 1 O THR A 619 N ALA A 592 LINK OG SER A 480 MG MG A1004 1555 1555 2.25 LINK OE1 GLN A 510 MG MG A1004 1555 1555 2.24 LINK O2G ATP A1001 MG MG A1002 1555 1555 2.14 LINK O1B ATP A1001 MG MG A1002 1555 1555 2.25 LINK O3G ATP A1003 MG MG A1004 1555 1555 2.14 LINK O2B ATP A1003 MG MG A1004 1555 1555 2.70 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 -1.000000 0.000000 0.000000 332.00012 MTRIX2 2 0.000000 -1.000000 0.000000 332.00012 MTRIX3 2 0.000000 0.000000 1.000000 0.00000 CONECT 3261 4739 CONECT 3509 4739 CONECT 4676 4677 4678 4679 4683 CONECT 4677 4676 CONECT 4678 4676 4707 CONECT 4679 4676 CONECT 4680 4681 4682 4683 4687 CONECT 4681 4680 4707 CONECT 4682 4680 CONECT 4683 4676 4680 CONECT 4684 4685 4686 4687 4688 CONECT 4685 4684 CONECT 4686 4684 CONECT 4687 4680 4684 CONECT 4688 4684 4689 CONECT 4689 4688 4690 CONECT 4690 4689 4691 4692 CONECT 4691 4690 4696 CONECT 4692 4690 4693 4694 CONECT 4693 4692 CONECT 4694 4692 4695 4696 CONECT 4695 4694 CONECT 4696 4691 4694 4697 CONECT 4697 4696 4698 4706 CONECT 4698 4697 4699 CONECT 4699 4698 4700 CONECT 4700 4699 4701 4706 CONECT 4701 4700 4702 4703 CONECT 4702 4701 CONECT 4703 4701 4704 CONECT 4704 4703 4705 CONECT 4705 4704 4706 CONECT 4706 4697 4700 4705 CONECT 4707 4678 4681 CONECT 4708 4709 4710 4711 4715 CONECT 4709 4708 CONECT 4710 4708 CONECT 4711 4708 4739 CONECT 4712 4713 4714 4715 4719 CONECT 4713 4712 CONECT 4714 4712 4739 CONECT 4715 4708 4712 CONECT 4716 4717 4718 4719 4720 CONECT 4717 4716 CONECT 4718 4716 CONECT 4719 4712 4716 CONECT 4720 4716 4721 CONECT 4721 4720 4722 CONECT 4722 4721 4723 4724 CONECT 4723 4722 4728 CONECT 4724 4722 4725 4726 CONECT 4725 4724 CONECT 4726 4724 4727 4728 CONECT 4727 4726 CONECT 4728 4723 4726 4729 CONECT 4729 4728 4730 4738 CONECT 4730 4729 4731 CONECT 4731 4730 4732 CONECT 4732 4731 4733 4738 CONECT 4733 4732 4734 4735 CONECT 4734 4733 CONECT 4735 4733 4736 CONECT 4736 4735 4737 CONECT 4737 4736 4738 CONECT 4738 4729 4732 4737 CONECT 4739 3261 3509 4711 4714 CONECT 4740 4741 4749 CONECT 4741 4740 4742 CONECT 4742 4741 4743 4767 CONECT 4743 4742 4744 CONECT 4744 4743 4745 4749 CONECT 4745 4744 4746 CONECT 4746 4745 4747 CONECT 4747 4746 4748 4753 CONECT 4748 4747 4749 4750 CONECT 4749 4740 4744 4748 4758 CONECT 4750 4748 4751 CONECT 4751 4750 4752 CONECT 4752 4751 4753 4756 4757 CONECT 4753 4747 4752 4754 CONECT 4754 4753 4755 CONECT 4755 4754 4756 CONECT 4756 4752 4755 4759 CONECT 4757 4752 CONECT 4758 4749 CONECT 4759 4756 4760 4761 CONECT 4760 4759 CONECT 4761 4759 4762 CONECT 4762 4761 4763 CONECT 4763 4762 4764 CONECT 4764 4763 4765 4766 CONECT 4765 4764 CONECT 4766 4764 CONECT 4767 4742 CONECT 4768 4769 4777 CONECT 4769 4768 4770 CONECT 4770 4769 4771 4795 CONECT 4771 4770 4772 CONECT 4772 4771 4773 4777 CONECT 4773 4772 4774 CONECT 4774 4773 4775 CONECT 4775 4774 4776 4781 CONECT 4776 4775 4777 4778 CONECT 4777 4768 4772 4776 4786 CONECT 4778 4776 4779 CONECT 4779 4778 4780 CONECT 4780 4779 4781 4784 4785 CONECT 4781 4775 4780 4782 CONECT 4782 4781 4783 CONECT 4783 4782 4784 CONECT 4784 4780 4783 4787 CONECT 4785 4780 CONECT 4786 4777 CONECT 4787 4784 4788 4789 CONECT 4788 4787 CONECT 4789 4787 4790 CONECT 4790 4789 4791 CONECT 4791 4790 4792 CONECT 4792 4791 4793 4794 CONECT 4793 4792 CONECT 4794 4792 CONECT 4795 4770 MASTER 530 0 6 21 12 0 0 12 4794 1 122 71 END