HEADER PROTEIN TRANSPORT 20-MAR-17 5V7V TITLE CRYO-EM STRUCTURE OF ERAD-ASSOCIATED E3 UBIQUITIN-PROTEIN LIGASE TITLE 2 COMPONENT HRD3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ERAD-ASSOCIATED E3 UBIQUITIN-PROTEIN LIGASE COMPONENT HRD3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-767; COMPND 5 SYNONYM: HMG-COA REDUCTASE DEGRADATION PROTEIN 3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / SOURCE 3 S288C); SOURCE 4 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 5 ORGANISM_TAXID: 559292; SOURCE 6 STRAIN: ATCC 204508 / S288C; SOURCE 7 GENE: HRD3, YLR207W; SOURCE 8 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 4932 KEYWDS HRD3 ERAD, PROTEIN TRANSPORT EXPDTA ELECTRON MICROSCOPY AUTHOR W.MI,S.SCHOEBEL,A.STEIN,T.A.RAPOPORT,M.LIAO REVDAT 6 29-JUL-20 5V7V 1 COMPND REMARK HETNAM LINK REVDAT 6 2 1 SITE ATOM REVDAT 5 01-JAN-20 5V7V 1 REMARK REVDAT 4 18-JUL-18 5V7V 1 REMARK REVDAT 3 30-AUG-17 5V7V 1 JRNL REVDAT 2 23-AUG-17 5V7V 1 JRNL REVDAT 1 16-AUG-17 5V7V 0 JRNL AUTH S.SCHOEBEL,W.MI,A.STEIN,S.OVCHINNIKOV,R.PAVLOVICZ,F.DIMAIO, JRNL AUTH 2 D.BAKER,M.G.CHAMBERS,H.SU,D.LI,T.A.RAPOPORT,M.LIAO JRNL TITL CRYO-EM STRUCTURE OF THE PROTEIN-CONDUCTING ERAD CHANNEL JRNL TITL 2 HRD1 IN COMPLEX WITH HRD3. JRNL REF NATURE V. 548 352 2017 JRNL REFN ESSN 1476-4687 JRNL PMID 28682307 JRNL DOI 10.1038/NATURE23314 REMARK 2 REMARK 2 RESOLUTION. 3.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION 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) : 3.900 REMARK 3 NUMBER OF PARTICLES : 204578 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 5V7V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1000226972. 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 : HRD1/HRD3 COMPLEX REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.80 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL 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) : 82.00 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 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 ILE A 2 REMARK 465 THR A 3 REMARK 465 LEU A 4 REMARK 465 LEU A 5 REMARK 465 LEU A 6 REMARK 465 TYR A 7 REMARK 465 LEU A 8 REMARK 465 CYS A 9 REMARK 465 VAL A 10 REMARK 465 ILE A 11 REMARK 465 CYS A 12 REMARK 465 ASN A 13 REMARK 465 ALA A 14 REMARK 465 ILE A 15 REMARK 465 VAL A 16 REMARK 465 LEU A 17 REMARK 465 ILE A 18 REMARK 465 ARG A 19 REMARK 465 ALA A 20 REMARK 465 ASP A 21 REMARK 465 SER A 22 REMARK 465 ILE A 23 REMARK 465 ALA A 24 REMARK 465 ASP A 25 REMARK 465 THR A 269 REMARK 465 ARG A 270 REMARK 465 PRO A 271 REMARK 465 ASP A 272 REMARK 465 ILE A 273 REMARK 465 GLY A 274 REMARK 465 SER A 275 REMARK 465 PRO A 276 REMARK 465 PHE A 277 REMARK 465 ILE A 278 REMARK 465 ALA A 279 REMARK 465 GLN A 280 REMARK 465 VAL A 281 REMARK 465 ASN A 282 REMARK 465 GLY A 283 REMARK 465 VAL A 284 REMARK 465 GLN A 285 REMARK 465 MET A 286 REMARK 465 THR A 287 REMARK 465 LEU A 288 REMARK 465 GLN A 289 REMARK 465 ILE A 290 REMARK 465 GLU A 291 REMARK 465 PRO A 292 REMARK 465 MET A 293 REMARK 465 GLY A 294 REMARK 465 ARG A 295 REMARK 465 PHE A 296 REMARK 465 ALA A 297 REMARK 465 PHE A 298 REMARK 465 ASN A 299 REMARK 465 GLY A 300 REMARK 465 ASN A 301 REMARK 465 ASP A 302 REMARK 465 GLY A 303 REMARK 465 ASN A 304 REMARK 465 ILE A 305 REMARK 465 ASN A 306 REMARK 465 GLY A 307 REMARK 465 ASP A 308 REMARK 465 GLU A 309 REMARK 465 ASP A 310 REMARK 465 ASP A 311 REMARK 465 GLU A 312 REMARK 465 ASP A 313 REMARK 465 ALA A 314 REMARK 465 SER A 315 REMARK 465 GLU A 316 REMARK 465 ARG A 687 REMARK 465 GLU A 688 REMARK 465 LYS A 689 REMARK 465 VAL A 690 REMARK 465 ASN A 691 REMARK 465 TYR A 692 REMARK 465 TRP A 693 REMARK 465 LYS A 694 REMARK 465 PRO A 695 REMARK 465 SER A 696 REMARK 465 SER A 697 REMARK 465 PRO A 698 REMARK 465 LEU A 699 REMARK 465 ASN A 700 REMARK 465 PRO A 701 REMARK 465 ASN A 702 REMARK 465 GLU A 703 REMARK 465 ASP A 704 REMARK 465 THR A 705 REMARK 465 GLN A 706 REMARK 465 HIS A 707 REMARK 465 SER A 708 REMARK 465 LYS A 709 REMARK 465 THR A 710 REMARK 465 SER A 711 REMARK 465 TRP A 712 REMARK 465 TYR A 713 REMARK 465 LYS A 714 REMARK 465 GLN A 715 REMARK 465 LEU A 716 REMARK 465 THR A 717 REMARK 465 LYS A 718 REMARK 465 ILE A 719 REMARK 465 LEU A 720 REMARK 465 GLN A 721 REMARK 465 ARG A 722 REMARK 465 MET A 723 REMARK 465 ARG A 724 REMARK 465 HIS A 725 REMARK 465 LYS A 726 REMARK 465 GLU A 727 REMARK 465 ASP A 728 REMARK 465 SER A 729 REMARK 465 ASP A 730 REMARK 465 LYS A 731 REMARK 465 ALA A 732 REMARK 465 ALA A 733 REMARK 465 GLU A 734 REMARK 465 ASP A 735 REMARK 465 SER A 736 REMARK 465 HIS A 737 REMARK 465 LYS A 738 REMARK 465 HIS A 739 REMARK 465 ARG A 740 REMARK 465 THR A 741 REMARK 465 VAL A 742 REMARK 465 VAL A 743 REMARK 465 GLN A 744 REMARK 465 ASN A 745 REMARK 465 GLY A 746 REMARK 465 ALA A 747 REMARK 465 ASN A 748 REMARK 465 HIS A 749 REMARK 465 ARG A 750 REMARK 465 GLY A 751 REMARK 465 ASP A 752 REMARK 465 ASP A 753 REMARK 465 GLN A 754 REMARK 465 GLU A 755 REMARK 465 GLU A 756 REMARK 465 ALA A 757 REMARK 465 SER A 758 REMARK 465 GLU A 759 REMARK 465 ILE A 760 REMARK 465 LEU A 761 REMARK 465 GLY A 762 REMARK 465 PHE A 763 REMARK 465 GLN A 764 REMARK 465 MET A 765 REMARK 465 GLU A 766 REMARK 465 ASP A 767 REMARK 465 GLY A 768 REMARK 465 GLY A 769 REMARK 465 GLY A 770 REMARK 465 GLU A 771 REMARK 465 ASN A 772 REMARK 465 LEU A 773 REMARK 465 TYR A 774 REMARK 465 PHE A 775 REMARK 465 GLN A 776 REMARK 465 SER A 777 REMARK 465 GLY A 778 REMARK 465 GLY A 779 REMARK 465 GLY A 780 REMARK 465 MET A 781 REMARK 465 ASP A 782 REMARK 465 GLU A 783 REMARK 465 LYS A 784 REMARK 465 THR A 785 REMARK 465 THR A 786 REMARK 465 GLY A 787 REMARK 465 TRP A 788 REMARK 465 ARG A 789 REMARK 465 GLY A 790 REMARK 465 GLY A 791 REMARK 465 HIS A 792 REMARK 465 VAL A 793 REMARK 465 VAL A 794 REMARK 465 GLU A 795 REMARK 465 GLY A 796 REMARK 465 LEU A 797 REMARK 465 ALA A 798 REMARK 465 GLY A 799 REMARK 465 GLU A 800 REMARK 465 LEU A 801 REMARK 465 GLU A 802 REMARK 465 GLN A 803 REMARK 465 LEU A 804 REMARK 465 ARG A 805 REMARK 465 ALA A 806 REMARK 465 ARG A 807 REMARK 465 LEU A 808 REMARK 465 GLU A 809 REMARK 465 HIS A 810 REMARK 465 HIS A 811 REMARK 465 PRO A 812 REMARK 465 GLN A 813 REMARK 465 GLY A 814 REMARK 465 GLN A 815 REMARK 465 ARG A 816 REMARK 465 GLU A 817 REMARK 465 PRO A 818 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 39 CG CD CE NZ REMARK 470 MET A 496 CG SD CE REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 H62 NAG B 1 O7 NAG B 2 1.07 REMARK 500 HB2 SER A 40 HE22 GLN A 117 1.10 REMARK 500 HD2 TYR A 612 HB3 LEU A 642 1.14 REMARK 500 HD22 ASN A 102 HG3 GLU A 104 1.20 REMARK 500 HD13 ILE A 37 HD1 TYR A 118 1.22 REMARK 500 HB2 SER A 40 NE2 GLN A 117 1.24 REMARK 500 HZ3 LYS A 133 H83 NAG A 901 1.25 REMARK 500 HD11 ILE A 37 HE1 TYR A 118 1.28 REMARK 500 HG2 GLN A 86 HE1 PHE A 120 1.31 REMARK 500 HD2 TYR A 107 HO6 NAG C 1 1.32 REMARK 500 HB2 SER A 103 HD12 LEU A 137 1.34 REMARK 500 HD2 TYR A 107 O6 NAG C 1 1.34 REMARK 500 O SER A 96 H PHE A 100 1.39 REMARK 500 O LEU A 92 H SER A 96 1.49 REMARK 500 HO3 NAG C 1 O5 NAG C 2 1.58 REMARK 500 CG TRP A 27 OE2 GLU A 104 1.71 REMARK 500 CD2 TRP A 27 OE2 GLU A 104 1.90 REMARK 500 C6 NAG B 1 O7 NAG B 2 2.01 REMARK 500 OD2 ASP A 42 NH1 ARG A 525 2.03 REMARK 500 O HIS A 378 OG1 THR A 382 2.04 REMARK 500 O VAL A 502 OG1 THR A 505 2.07 REMARK 500 OD2 ASP A 231 OH TYR A 425 2.07 REMARK 500 O LEU A 347 OG1 THR A 350 2.07 REMARK 500 O LEU A 398 OG SER A 401 2.07 REMARK 500 O GLN A 432 OG SER A 435 2.07 REMARK 500 CD1 TRP A 27 OE2 GLU A 104 2.09 REMARK 500 CB SER A 40 NE2 GLN A 117 2.10 REMARK 500 O GLN A 578 OG1 THR A 581 2.12 REMARK 500 O LEU A 472 OG1 THR A 475 2.13 REMARK 500 O ASN A 339 NH1 ARG A 342 2.14 REMARK 500 O THR A 553 OG SER A 557 2.16 REMARK 500 CD2 TYR A 107 O6 NAG C 1 2.17 REMARK 500 O GLU A 639 NH1 ARG A 646 2.18 REMARK 500 ND2 ASN A 611 O5 NAG A 909 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG A 646 CZ ARG A 646 NH1 0.090 REMARK 500 ARG A 646 CZ ARG A 646 NH2 0.094 REMARK 500 REMARK 500 REMARK: NULL 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 ASN A 102 N - CA - CB ANGL. DEV. = 15.9 DEGREES REMARK 500 SER A 116 N - CA - CB ANGL. DEV. = 12.8 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 LYS A 39 -166.98 -103.03 REMARK 500 TYR A 60 146.06 178.51 REMARK 500 SER A 66 71.49 59.82 REMARK 500 ASN A 101 41.50 -67.21 REMARK 500 SER A 103 -12.21 80.26 REMARK 500 THR A 138 66.58 60.17 REMARK 500 PRO A 204 -172.22 -69.21 REMARK 500 SER A 245 -5.23 83.07 REMARK 500 GLU A 248 -165.80 -79.10 REMARK 500 ASN A 257 -168.81 -125.66 REMARK 500 VAL A 259 69.57 62.78 REMARK 500 TYR A 334 -60.18 -100.81 REMARK 500 ASP A 359 -158.21 -94.66 REMARK 500 ASP A 362 81.57 61.66 REMARK 500 ALA A 408 -8.46 76.12 REMARK 500 ASN A 428 33.58 -143.94 REMARK 500 ASN A 447 -68.12 -92.03 REMARK 500 PRO A 462 84.00 -69.45 REMARK 500 GLU A 517 -6.15 74.26 REMARK 500 ALA A 530 5.43 -69.78 REMARK 500 ASP A 534 -172.75 -175.66 REMARK 500 ASP A 571 141.49 -174.18 REMARK 500 ASN A 595 93.90 -69.53 REMARK 500 ASN A 611 41.56 72.26 REMARK 500 LYS A 625 34.39 -97.25 REMARK 500 TYR A 626 64.20 64.02 REMARK 500 ILE A 628 -56.81 -127.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 LEU A 93 11.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 NAG A 901 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-8642 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF ERAD-ASSOCIATED E3 UBIQUITIN-PROTEIN LIGASE REMARK 900 COMPONENT HRD3 REMARK 900 RELATED ID: EMD-8637 RELATED DB: EMDB REMARK 900 CRYOEM STRUCTURE OF THE ERAD-ASSOCIATED E3 UBIQUITIN-PROTEIN LIGASE REMARK 900 HRD1 REMARK 900 RELATED ID: EMD-8638 RELATED DB: EMDB REMARK 900 CRYO-EM MAP OF THE ERAD COMPONENTS HRD1/HRD3 DIMER REMARK 900 RELATED ID: EMD-8639 RELATED DB: EMDB REMARK 900 CRYOEM MAP OF HRD1 DIMER WITH ONE HRD3 MOLECULE REMARK 900 RELATED ID: 5V6P RELATED DB: PDB REMARK 900 CRYO-ELECTRON MICROSCOPY STRUCTURE OF A COMPLEX OF THE ERAD REMARK 900 COMPONENTS HRD1 AND HRD3 DBREF 5V7V A 1 767 UNP Q05787 HRD3_YEAST 1 767 SEQADV 5V7V GLY A 768 UNP Q05787 EXPRESSION TAG SEQADV 5V7V GLY A 769 UNP Q05787 EXPRESSION TAG SEQADV 5V7V GLY A 770 UNP Q05787 EXPRESSION TAG SEQADV 5V7V GLU A 771 UNP Q05787 EXPRESSION TAG SEQADV 5V7V ASN A 772 UNP Q05787 EXPRESSION TAG SEQADV 5V7V LEU A 773 UNP Q05787 EXPRESSION TAG SEQADV 5V7V TYR A 774 UNP Q05787 EXPRESSION TAG SEQADV 5V7V PHE A 775 UNP Q05787 EXPRESSION TAG SEQADV 5V7V GLN A 776 UNP Q05787 EXPRESSION TAG SEQADV 5V7V SER A 777 UNP Q05787 EXPRESSION TAG SEQADV 5V7V GLY A 778 UNP Q05787 EXPRESSION TAG SEQADV 5V7V GLY A 779 UNP Q05787 EXPRESSION TAG SEQADV 5V7V GLY A 780 UNP Q05787 EXPRESSION TAG SEQADV 5V7V MET A 781 UNP Q05787 EXPRESSION TAG SEQADV 5V7V ASP A 782 UNP Q05787 EXPRESSION TAG SEQADV 5V7V GLU A 783 UNP Q05787 EXPRESSION TAG SEQADV 5V7V LYS A 784 UNP Q05787 EXPRESSION TAG SEQADV 5V7V THR A 785 UNP Q05787 EXPRESSION TAG SEQADV 5V7V THR A 786 UNP Q05787 EXPRESSION TAG SEQADV 5V7V GLY A 787 UNP Q05787 EXPRESSION TAG SEQADV 5V7V TRP A 788 UNP Q05787 EXPRESSION TAG SEQADV 5V7V ARG A 789 UNP Q05787 EXPRESSION TAG SEQADV 5V7V GLY A 790 UNP Q05787 EXPRESSION TAG SEQADV 5V7V GLY A 791 UNP Q05787 EXPRESSION TAG SEQADV 5V7V HIS A 792 UNP Q05787 EXPRESSION TAG SEQADV 5V7V VAL A 793 UNP Q05787 EXPRESSION TAG SEQADV 5V7V VAL A 794 UNP Q05787 EXPRESSION TAG SEQADV 5V7V GLU A 795 UNP Q05787 EXPRESSION TAG SEQADV 5V7V GLY A 796 UNP Q05787 EXPRESSION TAG SEQADV 5V7V LEU A 797 UNP Q05787 EXPRESSION TAG SEQADV 5V7V ALA A 798 UNP Q05787 EXPRESSION TAG SEQADV 5V7V GLY A 799 UNP Q05787 EXPRESSION TAG SEQADV 5V7V GLU A 800 UNP Q05787 EXPRESSION TAG SEQADV 5V7V LEU A 801 UNP Q05787 EXPRESSION TAG SEQADV 5V7V GLU A 802 UNP Q05787 EXPRESSION TAG SEQADV 5V7V GLN A 803 UNP Q05787 EXPRESSION TAG SEQADV 5V7V LEU A 804 UNP Q05787 EXPRESSION TAG SEQADV 5V7V ARG A 805 UNP Q05787 EXPRESSION TAG SEQADV 5V7V ALA A 806 UNP Q05787 EXPRESSION TAG SEQADV 5V7V ARG A 807 UNP Q05787 EXPRESSION TAG SEQADV 5V7V LEU A 808 UNP Q05787 EXPRESSION TAG SEQADV 5V7V GLU A 809 UNP Q05787 EXPRESSION TAG SEQADV 5V7V HIS A 810 UNP Q05787 EXPRESSION TAG SEQADV 5V7V HIS A 811 UNP Q05787 EXPRESSION TAG SEQADV 5V7V PRO A 812 UNP Q05787 EXPRESSION TAG SEQADV 5V7V GLN A 813 UNP Q05787 EXPRESSION TAG SEQADV 5V7V GLY A 814 UNP Q05787 EXPRESSION TAG SEQADV 5V7V GLN A 815 UNP Q05787 EXPRESSION TAG SEQADV 5V7V ARG A 816 UNP Q05787 EXPRESSION TAG SEQADV 5V7V GLU A 817 UNP Q05787 EXPRESSION TAG SEQADV 5V7V PRO A 818 UNP Q05787 EXPRESSION TAG SEQRES 1 A 818 MET ILE THR LEU LEU LEU TYR LEU CYS VAL ILE CYS ASN SEQRES 2 A 818 ALA ILE VAL LEU ILE ARG ALA ASP SER ILE ALA ASP PRO SEQRES 3 A 818 TRP PRO GLU ALA ARG HIS LEU LEU ASN THR ILE ALA LYS SEQRES 4 A 818 SER ARG ASP PRO MET LYS GLU ALA ALA MET GLU PRO ASN SEQRES 5 A 818 ALA ASP GLU PHE VAL GLY PHE TYR VAL PRO MET ASP TYR SEQRES 6 A 818 SER PRO ARG ASN GLU GLU LYS ASN TYR GLN SER ILE TRP SEQRES 7 A 818 GLN ASN GLU ILE THR ASP SER GLN ARG HIS ILE TYR GLU SEQRES 8 A 818 LEU LEU VAL GLN SER SER GLU GLN PHE ASN ASN SER GLU SEQRES 9 A 818 ALA THR TYR THR LEU SER GLN ILE HIS LEU TRP SER GLN SEQRES 10 A 818 TYR ASN PHE PRO HIS ASN MET THR LEU ALA HIS LYS TYR SEQRES 11 A 818 LEU GLU LYS PHE ASN ASP LEU THR HIS PHE THR ASN HIS SEQRES 12 A 818 SER ALA ILE PHE ASP LEU ALA VAL MET TYR ALA THR GLY SEQRES 13 A 818 GLY CYS ALA SER GLY ASN ASP GLN THR VAL ILE PRO GLN SEQRES 14 A 818 ASP SER ALA LYS ALA LEU LEU TYR TYR GLN ARG ALA ALA SEQRES 15 A 818 GLN LEU GLY ASN LEU LYS ALA LYS GLN VAL LEU ALA TYR SEQRES 16 A 818 LYS TYR TYR SER GLY PHE ASN VAL PRO ARG ASN PHE HIS SEQRES 17 A 818 LYS SER LEU VAL LEU TYR ARG ASP ILE ALA GLU GLN LEU SEQRES 18 A 818 ARG LYS SER TYR SER ARG ASP GLU TRP ASP ILE VAL PHE SEQRES 19 A 818 PRO TYR TRP GLU SER TYR ASN VAL ARG ILE SER ASP PHE SEQRES 20 A 818 GLU SER GLY LEU LEU GLY LYS GLY LEU ASN SER VAL PRO SEQRES 21 A 818 SER SER THR VAL ARG LYS ARG THR THR ARG PRO ASP ILE SEQRES 22 A 818 GLY SER PRO PHE ILE ALA GLN VAL ASN GLY VAL GLN MET SEQRES 23 A 818 THR LEU GLN ILE GLU PRO MET GLY ARG PHE ALA PHE ASN SEQRES 24 A 818 GLY ASN ASP GLY ASN ILE ASN GLY ASP GLU ASP ASP GLU SEQRES 25 A 818 ASP ALA SER GLU ARG ARG ILE ILE ARG ILE TYR TYR ALA SEQRES 26 A 818 ALA LEU ASN ASP TYR LYS GLY THR TYR SER GLN SER ARG SEQRES 27 A 818 ASN CYS GLU ARG ALA LYS ASN LEU LEU GLU LEU THR TYR SEQRES 28 A 818 LYS GLU PHE GLN PRO HIS VAL ASP ASN LEU ASP PRO LEU SEQRES 29 A 818 GLN VAL PHE TYR TYR VAL ARG CYS LEU GLN LEU LEU GLY SEQRES 30 A 818 HIS MET TYR PHE THR GLY GLU GLY SER SER LYS PRO ASN SEQRES 31 A 818 ILE HIS MET ALA GLU GLU ILE LEU THR THR SER LEU GLU SEQRES 32 A 818 ILE SER ARG ARG ALA GLN GLY PRO ILE GLY ARG ALA CYS SEQRES 33 A 818 ILE ASP LEU GLY LEU ILE ASN GLN TYR ILE THR ASN ASN SEQRES 34 A 818 ILE SER GLN ALA ILE SER TYR TYR MET LYS ALA MET LYS SEQRES 35 A 818 THR GLN ALA ASN ASN GLY ILE VAL GLU PHE GLN LEU SER SEQRES 36 A 818 LYS LEU ALA THR SER PHE PRO GLU GLU LYS ILE GLY ASP SEQRES 37 A 818 PRO PHE ASN LEU MET GLU THR ALA TYR LEU ASN GLY PHE SEQRES 38 A 818 ILE PRO ALA ILE TYR GLU PHE ALA VAL MET ILE GLU SER SEQRES 39 A 818 GLY MET ASN SER LYS SER SER VAL GLU ASN THR ALA TYR SEQRES 40 A 818 LEU PHE LYS THR PHE VAL ASP LYS ASN GLU ALA ILE MET SEQRES 41 A 818 ALA PRO LYS LEU ARG THR ALA PHE ALA ALA LEU ILE ASN SEQRES 42 A 818 ASP ARG SER GLU VAL ALA LEU TRP ALA TYR SER GLN LEU SEQRES 43 A 818 ALA GLU GLN GLY TYR GLU THR ALA GLN VAL SER ALA ALA SEQRES 44 A 818 TYR LEU MET TYR GLN LEU PRO TYR GLU PHE GLU ASP PRO SEQRES 45 A 818 PRO ARG THR THR ASP GLN ARG LYS THR LEU ALA ILE SER SEQRES 46 A 818 TYR TYR THR ARG ALA PHE LYS GLN GLY ASN ILE ASP ALA SEQRES 47 A 818 GLY VAL VAL ALA GLY ASP ILE TYR PHE GLN MET GLN ASN SEQRES 48 A 818 TYR SER LYS ALA MET ALA LEU TYR GLN GLY ALA ALA LEU SEQRES 49 A 818 LYS TYR SER ILE GLN ALA ILE TRP ASN LEU GLY TYR MET SEQRES 50 A 818 HIS GLU HIS GLY LEU GLY VAL ASN ARG ASP PHE HIS LEU SEQRES 51 A 818 ALA LYS ARG TYR TYR ASP GLN VAL SER GLU HIS ASP HIS SEQRES 52 A 818 ARG PHE TYR LEU ALA SER LYS LEU SER VAL LEU LYS LEU SEQRES 53 A 818 HIS LEU LYS SER TRP LEU THR TRP ILE THR ARG GLU LYS SEQRES 54 A 818 VAL ASN TYR TRP LYS PRO SER SER PRO LEU ASN PRO ASN SEQRES 55 A 818 GLU ASP THR GLN HIS SER LYS THR SER TRP TYR LYS GLN SEQRES 56 A 818 LEU THR LYS ILE LEU GLN ARG MET ARG HIS LYS GLU ASP SEQRES 57 A 818 SER ASP LYS ALA ALA GLU ASP SER HIS LYS HIS ARG THR SEQRES 58 A 818 VAL VAL GLN ASN GLY ALA ASN HIS ARG GLY ASP ASP GLN SEQRES 59 A 818 GLU GLU ALA SER GLU ILE LEU GLY PHE GLN MET GLU ASP SEQRES 60 A 818 GLY GLY GLY GLU ASN LEU TYR PHE GLN SER GLY GLY GLY SEQRES 61 A 818 MET ASP GLU LYS THR THR GLY TRP ARG GLY GLY HIS VAL SEQRES 62 A 818 VAL GLU GLY LEU ALA GLY GLU LEU GLU GLN LEU ARG ALA SEQRES 63 A 818 ARG LEU GLU HIS HIS PRO GLN GLY GLN ARG GLU PRO HET NAG B 1 27 HET NAG B 2 27 HET BMA B 3 22 HET NAG C 1 27 HET NAG C 2 27 HET BMA C 3 22 HET NAG A 901 28 HET NAG A 908 28 HET NAG A 909 28 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE FORMUL 2 NAG 7(C8 H15 N O6) FORMUL 2 BMA 2(C6 H12 O6) HELIX 1 AA1 PRO A 26 ALA A 38 1 13 HELIX 2 AA2 ASP A 42 GLU A 50 1 9 HELIX 3 AA3 SER A 66 ASN A 80 1 15 HELIX 4 AA4 THR A 83 PHE A 100 1 18 HELIX 5 AA5 SER A 103 LEU A 114 1 12 HELIX 6 AA6 ASN A 123 LEU A 137 1 15 HELIX 7 AA7 ASN A 142 GLY A 156 1 15 HELIX 8 AA8 ASP A 170 GLY A 185 1 16 HELIX 9 AA9 ASN A 186 GLY A 200 1 15 HELIX 10 AB1 ASN A 206 TYR A 225 1 20 HELIX 11 AB2 SER A 226 VAL A 233 1 8 HELIX 12 AB3 ARG A 318 LYS A 331 1 14 HELIX 13 AB4 CYS A 340 GLN A 355 1 16 HELIX 14 AB5 ASP A 362 GLY A 383 1 22 HELIX 15 AB6 ASN A 390 ARG A 406 1 17 HELIX 16 AB7 ILE A 412 ILE A 426 1 15 HELIX 17 AB8 ASN A 429 ALA A 440 1 12 HELIX 18 AB9 GLY A 448 PHE A 461 1 14 HELIX 19 AC1 ASP A 468 LEU A 478 1 11 HELIX 20 AC2 ILE A 482 GLY A 495 1 14 HELIX 21 AC3 VAL A 502 GLU A 517 1 16 HELIX 22 AC4 LYS A 523 ASN A 533 1 11 HELIX 23 AC5 ARG A 535 ALA A 547 1 13 HELIX 24 AC6 TYR A 551 TYR A 563 1 13 HELIX 25 AC7 THR A 576 LYS A 592 1 17 HELIX 26 AC8 ASN A 595 MET A 609 1 15 HELIX 27 AC9 ASN A 611 LEU A 624 1 14 HELIX 28 AD1 ILE A 628 HIS A 640 1 13 HELIX 29 AD2 PHE A 648 HIS A 663 1 16 HELIX 30 AD3 PHE A 665 TRP A 684 1 20 LINK ND2 ASN A 123 C1 NAG B 1 1555 1555 1.44 LINK ND2 ASN A 142 C1 NAG C 1 1555 1555 1.46 LINK ND2 ASN A 429 C1 NAG A 908 1555 1555 1.45 LINK ND2 ASN A 611 C1 NAG A 909 1555 1555 1.43 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.37 LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.44 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.44 LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.46 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