HEADER MEMBRANE PROTEIN 21-SEP-21 7PQG TITLE STRUCTURE OF THERMOSTABILISED HUMAN NTCP IN COMPLEX WITH NANOBODY 87 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NANOBODY 87; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: SODIUM/BILE ACID COTRANSPORTER; COMPND 7 CHAIN: A; COMPND 8 SYNONYM: CELL GROWTH-INHIBITING GENE 29 PROTEIN,NA(+)/BILE ACID COMPND 9 COTRANSPORTER,NA(+)/TAUROCHOLATE TRANSPORT PROTEIN, COMPND 10 SODIUM/TAUROCHOLATE COTRANSPORTING POLYPEPTIDE,SOLUTE CARRIER FAMILY COMPND 11 10 MEMBER 1, NTCP; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 3 ORGANISM_TAXID: 9844; SOURCE 4 STRAIN: LAMA GLAMA; SOURCE 5 VARIANT: 9844; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: WK6; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: SLC10A1, NTCP, GIG29; SOURCE 14 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 16 EXPRESSION_SYSTEM_CELL_LINE: HEK293F KEYWDS SLC10A1, SODIUM BILE ACID SYMPORTER, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR K.GOUTAM,N.REYES REVDAT 2 06-JUL-22 7PQG 1 JRNL REVDAT 1 18-MAY-22 7PQG 0 JRNL AUTH K.GOUTAM,F.S.IELASI,E.PARDON,J.STEYAERT,N.REYES JRNL TITL STRUCTURAL BASIS OF SODIUM-DEPENDENT BILE SALT UPTAKE INTO JRNL TITL 2 THE LIVER. JRNL REF NATURE V. 606 1015 2022 JRNL REFN ESSN 1476-4687 JRNL PMID 35545671 JRNL DOI 10.1038/S41586-022-04723-Z REMARK 2 REMARK 2 RESOLUTION. 3.70 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) : 3.700 REMARK 3 NUMBER OF PARTICLES : 61053 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 7PQG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1292118120. 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 : HUMAN NTCP IN COMPLEX WITH REMARK 245 NANOBODY 87 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 : 7.40 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 K3 BIOQUANTUM (6K X REMARK 245 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) : 5780.00 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 SER B 125 REMARK 465 SER B 126 REMARK 465 HIS B 127 REMARK 465 HIS B 128 REMARK 465 HIS B 129 REMARK 465 HIS B 130 REMARK 465 HIS B 131 REMARK 465 HIS B 132 REMARK 465 GLU B 133 REMARK 465 PRO B 134 REMARK 465 GLU B 135 REMARK 465 ALA B 136 REMARK 465 MET A 2 REMARK 465 ALA A 3 REMARK 465 HIS A 4 REMARK 465 THR A 5 REMARK 465 ALA A 6 REMARK 465 SER A 7 REMARK 465 ALA A 8 REMARK 465 PRO A 9 REMARK 465 PHE A 10 REMARK 465 THR A 11 REMARK 465 LYS A 311 REMARK 465 THR A 312 REMARK 465 PRO A 313 REMARK 465 LYS A 314 REMARK 465 ASP A 315 REMARK 465 LYS A 316 REMARK 465 THR A 317 REMARK 465 LYS A 318 REMARK 465 MET A 319 REMARK 465 ILE A 320 REMARK 465 TYR A 321 REMARK 465 THR A 322 REMARK 465 ALA A 323 REMARK 465 ALA A 324 REMARK 465 THR A 325 REMARK 465 THR A 326 REMARK 465 GLU A 327 REMARK 465 GLU A 328 REMARK 465 LEU A 329 REMARK 465 GLU A 330 REMARK 465 VAL A 331 REMARK 465 LEU A 332 REMARK 465 PHE A 333 REMARK 465 GLN A 334 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 THR B 29 -169.32 -73.41 REMARK 500 VAL B 48 -57.70 -127.51 REMARK 500 THR A 13 41.39 39.23 REMARK 500 ARG A 84 48.55 37.28 REMARK 500 MET A 112 -63.52 -92.83 REMARK 500 TYR A 146 -58.32 -122.99 REMARK 500 PHE A 244 30.45 -91.90 REMARK 500 CYS A 245 19.20 58.46 REMARK 500 GLN A 261 -168.93 -108.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-13593 RELATED DB: EMDB REMARK 900 STRUCTURE OF HUMAN NTCP IN COMPLEX WITH NANOBODY 87 DBREF 7PQG B 1 136 PDB 7PQG 7PQG 1 136 DBREF 7PQG A 3 328 UNP Q14973 NTCP_HUMAN 3 328 SEQADV 7PQG MET A 2 UNP Q14973 INITIATING METHIONINE SEQADV 7PQG THR A 5 UNP Q14973 ASN 5 ENGINEERED MUTATION SEQADV 7PQG THR A 11 UNP Q14973 ASN 11 ENGINEERED MUTATION SEQADV 7PQG VAL A 33 UNP Q14973 PHE 33 ENGINEERED MUTATION SEQADV 7PQG ILE A 37 UNP Q14973 PHE 37 ENGINEERED MUTATION SEQADV 7PQG ASN A 86 UNP Q14973 LYS 86 ENGINEERED MUTATION SEQADV 7PQG ILE A 95 UNP Q14973 VAL 95 ENGINEERED MUTATION SEQADV 7PQG ILE A 107 UNP Q14973 VAL 107 ENGINEERED MUTATION SEQADV 7PQG LEU A 129 UNP Q14973 CYS 129 ENGINEERED MUTATION SEQADV 7PQG HIS A 221 UNP Q14973 LEU 221 ENGINEERED MUTATION SEQADV 7PQG LEU A 329 UNP Q14973 EXPRESSION TAG SEQADV 7PQG GLU A 330 UNP Q14973 EXPRESSION TAG SEQADV 7PQG VAL A 331 UNP Q14973 EXPRESSION TAG SEQADV 7PQG LEU A 332 UNP Q14973 EXPRESSION TAG SEQADV 7PQG PHE A 333 UNP Q14973 EXPRESSION TAG SEQADV 7PQG GLN A 334 UNP Q14973 EXPRESSION TAG SEQRES 1 B 136 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 B 136 ALA GLY GLY SER LEU ARG LEU SER CYS ALA VAL SER GLY SEQRES 3 B 136 ARG THR THR ALA ASN TYR ASN MET GLY TRP PHE ARG GLN SEQRES 4 B 136 ALA PRO GLY LYS GLU ARG GLU PHE VAL ALA GLY ILE LYS SEQRES 5 B 136 TRP SER SER GLY SER THR TYR VAL ALA ASP SER ALA LYS SEQRES 6 B 136 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN SER SEQRES 7 B 136 VAL TYR LEU GLN MET ASP SER LEU LYS PRO GLU ASP THR SEQRES 8 B 136 ALA LEU TYR TYR CYS ALA ALA ASN TYR TYR GLY VAL SER SEQRES 9 B 136 TRP PHE LEU ILE SER PRO SER SER TYR ASP TYR TRP GLY SEQRES 10 B 136 GLN GLY THR GLN VAL THR VAL SER SER HIS HIS HIS HIS SEQRES 11 B 136 HIS HIS GLU PRO GLU ALA SEQRES 1 A 333 MET ALA HIS THR ALA SER ALA PRO PHE THR PHE THR LEU SEQRES 2 A 333 PRO PRO ASN PHE GLY LYS ARG PRO THR ASP LEU ALA LEU SEQRES 3 A 333 SER VAL ILE LEU VAL VAL MET LEU PHE ILE ILE MET LEU SEQRES 4 A 333 SER LEU GLY CYS THR MET GLU PHE SER LYS ILE LYS ALA SEQRES 5 A 333 HIS LEU TRP LYS PRO LYS GLY LEU ALA ILE ALA LEU VAL SEQRES 6 A 333 ALA GLN TYR GLY ILE MET PRO LEU THR ALA PHE VAL LEU SEQRES 7 A 333 GLY LYS VAL PHE ARG LEU ASN ASN ILE GLU ALA LEU ALA SEQRES 8 A 333 ILE LEU ILE CYS GLY CYS SER PRO GLY GLY ASN LEU SER SEQRES 9 A 333 ASN ILE PHE SER LEU ALA MET LYS GLY ASP MET ASN LEU SEQRES 10 A 333 SER ILE VAL MET THR THR CYS SER THR PHE LEU ALA LEU SEQRES 11 A 333 GLY MET MET PRO LEU LEU LEU TYR ILE TYR SER ARG GLY SEQRES 12 A 333 ILE TYR ASP GLY ASP LEU LYS ASP LYS VAL PRO TYR LYS SEQRES 13 A 333 GLY ILE VAL ILE SER LEU VAL LEU VAL LEU ILE PRO CYS SEQRES 14 A 333 THR ILE GLY ILE VAL LEU LYS SER LYS ARG PRO GLN TYR SEQRES 15 A 333 MET ARG TYR VAL ILE LYS GLY GLY MET ILE ILE ILE LEU SEQRES 16 A 333 LEU CYS SER VAL ALA VAL THR VAL LEU SER ALA ILE ASN SEQRES 17 A 333 VAL GLY LYS SER ILE MET PHE ALA MET THR PRO HIS LEU SEQRES 18 A 333 ILE ALA THR SER SER LEU MET PRO PHE ILE GLY PHE LEU SEQRES 19 A 333 LEU GLY TYR VAL LEU SER ALA LEU PHE CYS LEU ASN GLY SEQRES 20 A 333 ARG CYS ARG ARG THR VAL SER MET GLU THR GLY CYS GLN SEQRES 21 A 333 ASN VAL GLN LEU CYS SER THR ILE LEU ASN VAL ALA PHE SEQRES 22 A 333 PRO PRO GLU VAL ILE GLY PRO LEU PHE PHE PHE PRO LEU SEQRES 23 A 333 LEU TYR MET ILE PHE GLN LEU GLY GLU GLY LEU LEU LEU SEQRES 24 A 333 ILE ALA ILE PHE TRP CYS TYR GLU LYS PHE LYS THR PRO SEQRES 25 A 333 LYS ASP LYS THR LYS MET ILE TYR THR ALA ALA THR THR SEQRES 26 A 333 GLU GLU LEU GLU VAL LEU PHE GLN HELIX 1 AA1 ASP B 62 LYS B 65 5 4 HELIX 2 AA2 LYS B 87 THR B 91 5 5 HELIX 3 AA3 SER B 109 TYR B 113 5 5 HELIX 4 AA4 LYS A 20 CYS A 44 1 25 HELIX 5 AA5 GLU A 47 LEU A 55 1 9 HELIX 6 AA6 PRO A 58 PHE A 83 1 26 HELIX 7 AA7 ASN A 86 CYS A 98 1 13 HELIX 8 AA8 GLY A 102 LYS A 113 1 12 HELIX 9 AA9 ASP A 115 ARG A 143 1 29 HELIX 10 AB1 GLY A 148 LYS A 153 5 6 HELIX 11 AB2 PRO A 155 LYS A 179 1 25 HELIX 12 AB3 ARG A 180 GLN A 182 5 3 HELIX 13 AB4 TYR A 183 VAL A 210 1 28 HELIX 14 AB5 GLY A 211 MET A 218 1 8 HELIX 15 AB6 THR A 219 PHE A 244 1 26 HELIX 16 AB7 ASN A 247 CYS A 260 1 14 HELIX 17 AB8 ASN A 262 PHE A 274 1 13 HELIX 18 AB9 PRO A 275 GLY A 280 1 6 HELIX 19 AC1 PRO A 281 PHE A 283 5 3 HELIX 20 AC2 PHE A 284 PHE A 310 1 27 SHEET 1 AA1 4 GLN B 3 LEU B 4 0 SHEET 2 AA1 4 LEU B 18 SER B 25 -1 O SER B 25 N GLN B 3 SHEET 3 AA1 4 SER B 78 MET B 83 -1 O VAL B 79 N CYS B 22 SHEET 4 AA1 4 SER B 71 ASP B 73 -1 N ASP B 73 O SER B 78 SHEET 1 AA2 5 THR B 58 VAL B 60 0 SHEET 2 AA2 5 ALA B 49 LYS B 52 -1 N GLY B 50 O TYR B 59 SHEET 3 AA2 5 ASN B 33 TRP B 36 -1 N TRP B 36 O ALA B 49 SHEET 4 AA2 5 CYS B 96 ASN B 99 -1 O ALA B 97 N GLY B 35 SHEET 5 AA2 5 TYR B 115 TRP B 116 -1 O TYR B 115 N ALA B 98 SHEET 1 AA3 2 ALA B 92 LEU B 93 0 SHEET 2 AA3 2 GLN B 121 VAL B 122 -1 O VAL B 122 N ALA B 92 SSBOND 1 CYS B 22 CYS B 96 1555 1555 2.03 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