HEADER TRANSPORT PROTEIN 13-SEP-24 9GRZ TITLE CRYO-EM STRUCTURE OF HUMAN SLC35B1 WITH AMP-PNP COMPND MOL_ID: 1; COMPND 2 MOLECULE: SOLUTE CARRIER FAMILY 35 MEMBER B1; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: ATP/ADP EXCHANGER ER,AXER,ENDOPLASMIC RETICULUM ATP/ADP COMPND 5 TRANSLOCASE,UDP-GALACTOSE TRANSPORTER-RELATED PROTEIN 1,UGTREL1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SLC35B1, UGTREL1; SOURCE 6 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4932 KEYWDS ATP:ADP EXCHANGER, AXER, AMP-PNP, MEMBRANE PROTEIN, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR A.GULATI,D.AHN,A.SUADES,D.DREW REVDAT 2 20-AUG-25 9GRZ 1 JRNL REVDAT 1 21-MAY-25 9GRZ 0 JRNL AUTH A.GULATI,D.H.AHN,A.SUADES,Y.HULT,G.WOLF,S.IWATA, JRNL AUTH 2 G.SUPERTI-FURGA,N.NOMURA,D.DREW JRNL TITL STEPWISE ATP TRANSLOCATION INTO THE ENDOPLASMIC RETICULUM BY JRNL TITL 2 HUMAN SLC35B1. JRNL REF NATURE V. 643 855 2025 JRNL REFN ESSN 1476-4687 JRNL PMID 40399679 JRNL DOI 10.1038/S41586-025-09069-W REMARK 2 REMARK 2 RESOLUTION. 3.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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) : 3.400 REMARK 3 NUMBER OF PARTICLES : 114510 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 9GRZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-SEP-24. REMARK 100 THE DEPOSITION ID IS D_1292141288. 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 : COMPLEX OF HUMAN SLC35B1 WITH REMARK 245 AMP-PNP 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 : 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 600.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 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) : 5900.00 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 B 1 REMARK 465 ALA B 2 REMARK 465 SER B 3 REMARK 465 SER B 4 REMARK 465 SER B 5 REMARK 465 SER B 6 REMARK 465 LEU B 7 REMARK 465 VAL B 8 REMARK 465 PRO B 9 REMARK 465 ASP B 10 REMARK 465 ARG B 11 REMARK 465 GLY B 41 REMARK 465 GLU B 42 REMARK 465 GLY B 43 REMARK 465 ALA B 44 REMARK 465 LYS B 45 REMARK 465 GLY B 163 REMARK 465 ILE B 164 REMARK 465 GLU B 165 REMARK 465 GLU B 166 REMARK 465 HIS B 167 REMARK 465 ALA B 317 REMARK 465 LYS B 318 REMARK 465 LYS B 319 REMARK 465 THR B 320 REMARK 465 SER B 321 REMARK 465 HIS B 322 REMARK 465 GLY B 323 REMARK 465 GLU B 324 REMARK 465 ASN B 325 REMARK 465 LEU B 326 REMARK 465 TYR B 327 REMARK 465 PHE B 328 REMARK 465 GLN B 329 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 ALA B 238 35.40 -99.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-51529 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF HUMAN SLC35B1 WITH AMP-PNP DBREF 9GRZ B 1 322 UNP P78383 S35B1_HUMAN 1 322 SEQADV 9GRZ HIS B 81 UNP P78383 ARG 81 VARIANT SEQADV 9GRZ GLY B 323 UNP P78383 EXPRESSION TAG SEQADV 9GRZ GLU B 324 UNP P78383 EXPRESSION TAG SEQADV 9GRZ ASN B 325 UNP P78383 EXPRESSION TAG SEQADV 9GRZ LEU B 326 UNP P78383 EXPRESSION TAG SEQADV 9GRZ TYR B 327 UNP P78383 EXPRESSION TAG SEQADV 9GRZ PHE B 328 UNP P78383 EXPRESSION TAG SEQADV 9GRZ GLN B 329 UNP P78383 EXPRESSION TAG SEQRES 1 B 329 MET ALA SER SER SER SER LEU VAL PRO ASP ARG LEU ARG SEQRES 2 B 329 LEU PRO LEU CYS PHE LEU GLY VAL PHE VAL CYS TYR PHE SEQRES 3 B 329 TYR TYR GLY ILE LEU GLN GLU LYS ILE THR ARG GLY LYS SEQRES 4 B 329 TYR GLY GLU GLY ALA LYS GLN GLU THR PHE THR PHE ALA SEQRES 5 B 329 LEU THR LEU VAL PHE ILE GLN CYS VAL ILE ASN ALA VAL SEQRES 6 B 329 PHE ALA LYS ILE LEU ILE GLN PHE PHE ASP THR ALA ARG SEQRES 7 B 329 VAL ASP HIS THR ARG SER TRP LEU TYR ALA ALA CYS SER SEQRES 8 B 329 ILE SER TYR LEU GLY ALA MET VAL SER SER ASN SER ALA SEQRES 9 B 329 LEU GLN PHE VAL ASN TYR PRO THR GLN VAL LEU GLY LYS SEQRES 10 B 329 SER CYS LYS PRO ILE PRO VAL MET LEU LEU GLY VAL THR SEQRES 11 B 329 LEU LEU LYS LYS LYS TYR PRO LEU ALA LYS TYR LEU CYS SEQRES 12 B 329 VAL LEU LEU ILE VAL ALA GLY VAL ALA LEU PHE MET TYR SEQRES 13 B 329 LYS PRO LYS LYS VAL VAL GLY ILE GLU GLU HIS THR VAL SEQRES 14 B 329 GLY TYR GLY GLU LEU LEU LEU LEU LEU SER LEU THR LEU SEQRES 15 B 329 ASP GLY LEU THR GLY VAL SER GLN ASP HIS MET ARG ALA SEQRES 16 B 329 HIS TYR GLN THR GLY SER ASN HIS MET MET LEU ASN ILE SEQRES 17 B 329 ASN LEU TRP SER THR LEU LEU LEU GLY MET GLY ILE LEU SEQRES 18 B 329 PHE THR GLY GLU LEU TRP GLU PHE LEU SER PHE ALA GLU SEQRES 19 B 329 ARG TYR PRO ALA ILE ILE TYR ASN ILE LEU LEU PHE GLY SEQRES 20 B 329 LEU THR SER ALA LEU GLY GLN SER PHE ILE PHE MET THR SEQRES 21 B 329 VAL VAL TYR PHE GLY PRO LEU THR CYS SER ILE ILE THR SEQRES 22 B 329 THR THR ARG LYS PHE PHE THR ILE LEU ALA SER VAL ILE SEQRES 23 B 329 LEU PHE ALA ASN PRO ILE SER PRO MET GLN TRP VAL GLY SEQRES 24 B 329 THR VAL LEU VAL PHE LEU GLY LEU GLY LEU ASP ALA LYS SEQRES 25 B 329 PHE GLY LYS GLY ALA LYS LYS THR SER HIS GLY GLU ASN SEQRES 26 B 329 LEU TYR PHE GLN HET ANP B 401 44 HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER FORMUL 2 ANP C10 H17 N6 O12 P3 HELIX 1 AA1 PRO B 15 ARG B 37 1 23 HELIX 2 AA2 ALA B 52 GLN B 72 1 21 HELIX 3 AA3 ARG B 83 ALA B 104 1 22 HELIX 4 AA4 LEU B 105 PHE B 107 5 3 HELIX 5 AA5 ASN B 109 LYS B 117 1 9 HELIX 6 AA6 LYS B 120 LEU B 131 1 12 HELIX 7 AA7 LEU B 142 MET B 155 1 14 HELIX 8 AA8 GLY B 170 HIS B 196 1 27 HELIX 9 AA9 SER B 201 GLY B 224 1 24 HELIX 10 AB1 GLU B 228 TYR B 236 1 9 HELIX 11 AB2 ILE B 240 VAL B 262 1 23 HELIX 12 AB3 PRO B 266 PHE B 288 1 23 HELIX 13 AB4 SER B 293 LEU B 307 1 15 HELIX 14 AB5 GLY B 308 PHE B 313 1 6 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 CONECT 4752 4753 4754 4755 4759 CONECT 4753 4752 CONECT 4754 4752 CONECT 4755 4752 CONECT 4756 4757 4758 4759 4763 CONECT 4757 4756 CONECT 4758 4756 CONECT 4759 4752 4756 4783 CONECT 4760 4761 4762 4763 4764 CONECT 4761 4760 CONECT 4762 4760 CONECT 4763 4756 4760 CONECT 4764 4760 4765 CONECT 4765 4764 4766 4784 4785 CONECT 4766 4765 4767 4768 4786 CONECT 4767 4766 4772 CONECT 4768 4766 4769 4770 4787 CONECT 4769 4768 4788 CONECT 4770 4768 4771 4772 4789 CONECT 4771 4770 4790 CONECT 4772 4767 4770 4773 4791 CONECT 4773 4772 4774 4782 CONECT 4774 4773 4775 4792 CONECT 4775 4774 4776 CONECT 4776 4775 4777 4782 CONECT 4777 4776 4778 4779 CONECT 4778 4777 4793 4794 CONECT 4779 4777 4780 CONECT 4780 4779 4781 4795 CONECT 4781 4780 4782 CONECT 4782 4773 4776 4781 CONECT 4783 4759 CONECT 4784 4765 CONECT 4785 4765 CONECT 4786 4766 CONECT 4787 4768 CONECT 4788 4769 CONECT 4789 4770 CONECT 4790 4771 CONECT 4791 4772 CONECT 4792 4774 CONECT 4793 4778 CONECT 4794 4778 CONECT 4795 4780 MASTER 160 0 1 14 0 0 0 6 2354 1 44 26 END