HEADER TRANSPORT PROTEIN 11-DEC-23 8VAF TITLE CRYOGENIC ELECTRON MICROSCOPY STRUCTURE OF APO HUMAN SERUM ALBUMIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERUM ALBUMIN; COMPND 3 CHAIN: A; COMPND 4 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: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, SOURCE 6 PRO2675, UNQ696/PRO1341; SOURCE 7 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS HUMAN SERUM ALBUMIN, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR C.CATALANO,K.W.LUCIER,D.TO,S.SENKO,N.L.TRAN,A.C.FARWELL,S.M.SILVA, AUTHOR 2 P.V.DIP,N.POWELEIT,G.SCAPIN REVDAT 1 26-JUN-24 8VAF 0 JRNL AUTH C.CATALANO,K.W.LUCIER,D.TO,S.SENKO,N.L.TRAN,A.C.FARWELL, JRNL AUTH 2 S.M.SILVA,P.V.DIP,N.POWELEIT,G.SCAPIN JRNL TITL THE CRYOEM STRUCTURE OF HUMAN SERUM ALBUMIN IN COMPLEX WITH JRNL TITL 2 LIGANDS. JRNL REF J.STRUCT.BIOL. V. 216 08105 2024 JRNL REFN ESSN 1095-8657 JRNL PMID 38852682 JRNL DOI 10.1016/J.JSB.2024.108105 REMARK 2 REMARK 2 RESOLUTION. 3.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, LEGINON, CRYOSPARC, UCSF REMARK 3 CHIMERAX, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 1AO6 REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT 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) : 3.500 REMARK 3 NUMBER OF PARTICLES : 54988 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 8VAF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1000279794. 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 : APO HUMAN SERUM ALBUMIN 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 : 5901 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS GLACIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4096.00 REMARK 245 ILLUMINATION MODE : SPOT SCAN REMARK 245 NOMINAL MAGNIFICATION : 240000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 200 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 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 ASP A 1 REMARK 465 LEU A 583 REMARK 465 GLY A 584 REMARK 465 LEU A 585 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 SG CYS A 316 SG CYS A 361 1.30 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 CYS A 289 CA - CB - SG ANGL. DEV. = 8.5 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 GLU A 82 -63.73 61.18 REMARK 500 ARG A 117 73.43 57.56 REMARK 500 ALA A 172 146.40 -174.20 REMARK 500 ILE A 271 -62.41 -104.03 REMARK 500 LEU A 305 -0.78 66.28 REMARK 500 ASP A 314 33.39 -95.49 REMARK 500 CYS A 361 0.12 -155.45 REMARK 500 LYS A 372 31.46 -97.05 REMARK 500 GLU A 442 47.27 -80.53 REMARK 500 ASP A 563 63.03 37.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-43090 RELATED DB: EMDB REMARK 900 CRYOGENIC ELECTRON MICROSCOPY STRUCTURE OF APO HUMAN SERUM ALBUMIN DBREF 8VAF A 1 585 UNP P02768 ALBU_HUMAN 25 609 SEQRES 1 A 585 ASP ALA HIS LYS SER GLU VAL ALA HIS ARG PHE LYS ASP SEQRES 2 A 585 LEU GLY GLU GLU ASN PHE LYS ALA LEU VAL LEU ILE ALA SEQRES 3 A 585 PHE ALA GLN TYR LEU GLN GLN CYS PRO PHE GLU ASP HIS SEQRES 4 A 585 VAL LYS LEU VAL ASN GLU VAL THR GLU PHE ALA LYS THR SEQRES 5 A 585 CYS VAL ALA ASP GLU SER ALA GLU ASN CYS ASP LYS SER SEQRES 6 A 585 LEU HIS THR LEU PHE GLY ASP LYS LEU CYS THR VAL ALA SEQRES 7 A 585 THR LEU ARG GLU THR TYR GLY GLU MET ALA ASP CYS CYS SEQRES 8 A 585 ALA LYS GLN GLU PRO GLU ARG ASN GLU CYS PHE LEU GLN SEQRES 9 A 585 HIS LYS ASP ASP ASN PRO ASN LEU PRO ARG LEU VAL ARG SEQRES 10 A 585 PRO GLU VAL ASP VAL MET CYS THR ALA PHE HIS ASP ASN SEQRES 11 A 585 GLU GLU THR PHE LEU LYS LYS TYR LEU TYR GLU ILE ALA SEQRES 12 A 585 ARG ARG HIS PRO TYR PHE TYR ALA PRO GLU LEU LEU PHE SEQRES 13 A 585 PHE ALA LYS ARG TYR LYS ALA ALA PHE THR GLU CYS CYS SEQRES 14 A 585 GLN ALA ALA ASP LYS ALA ALA CYS LEU LEU PRO LYS LEU SEQRES 15 A 585 ASP GLU LEU ARG ASP GLU GLY LYS ALA SER SER ALA LYS SEQRES 16 A 585 GLN ARG LEU LYS CYS ALA SER LEU GLN LYS PHE GLY GLU SEQRES 17 A 585 ARG ALA PHE LYS ALA TRP ALA VAL ALA ARG LEU SER GLN SEQRES 18 A 585 ARG PHE PRO LYS ALA GLU PHE ALA GLU VAL SER LYS LEU SEQRES 19 A 585 VAL THR ASP LEU THR LYS VAL HIS THR GLU CYS CYS HIS SEQRES 20 A 585 GLY ASP LEU LEU GLU CYS ALA ASP ASP ARG ALA ASP LEU SEQRES 21 A 585 ALA LYS TYR ILE CYS GLU ASN GLN ASP SER ILE SER SER SEQRES 22 A 585 LYS LEU LYS GLU CYS CYS GLU LYS PRO LEU LEU GLU LYS SEQRES 23 A 585 SER HIS CYS ILE ALA GLU VAL GLU ASN ASP GLU MET PRO SEQRES 24 A 585 ALA ASP LEU PRO SER LEU ALA ALA ASP PHE VAL GLU SER SEQRES 25 A 585 LYS ASP VAL CYS LYS ASN TYR ALA GLU ALA LYS ASP VAL SEQRES 26 A 585 PHE LEU GLY MET PHE LEU TYR GLU TYR ALA ARG ARG HIS SEQRES 27 A 585 PRO ASP TYR SER VAL VAL LEU LEU LEU ARG LEU ALA LYS SEQRES 28 A 585 THR TYR GLU THR THR LEU GLU LYS CYS CYS ALA ALA ALA SEQRES 29 A 585 ASP PRO HIS GLU CYS TYR ALA LYS VAL PHE ASP GLU PHE SEQRES 30 A 585 LYS PRO LEU VAL GLU GLU PRO GLN ASN LEU ILE LYS GLN SEQRES 31 A 585 ASN CYS GLU LEU PHE GLU GLN LEU GLY GLU TYR LYS PHE SEQRES 32 A 585 GLN ASN ALA LEU LEU VAL ARG TYR THR LYS LYS VAL PRO SEQRES 33 A 585 GLN VAL SER THR PRO THR LEU VAL GLU VAL SER ARG ASN SEQRES 34 A 585 LEU GLY LYS VAL GLY SER LYS CYS CYS LYS HIS PRO GLU SEQRES 35 A 585 ALA LYS ARG MET PRO CYS ALA GLU ASP TYR LEU SER VAL SEQRES 36 A 585 VAL LEU ASN GLN LEU CYS VAL LEU HIS GLU LYS THR PRO SEQRES 37 A 585 VAL SER ASP ARG VAL THR LYS CYS CYS THR GLU SER LEU SEQRES 38 A 585 VAL ASN ARG ARG PRO CYS PHE SER ALA LEU GLU VAL ASP SEQRES 39 A 585 GLU THR TYR VAL PRO LYS GLU PHE ASN ALA GLU THR PHE SEQRES 40 A 585 THR PHE HIS ALA ASP ILE CYS THR LEU SER GLU LYS GLU SEQRES 41 A 585 ARG GLN ILE LYS LYS GLN THR ALA LEU VAL GLU LEU VAL SEQRES 42 A 585 LYS HIS LYS PRO LYS ALA THR LYS GLU GLN LEU LYS ALA SEQRES 43 A 585 VAL MET ASP ASP PHE ALA ALA PHE VAL GLU LYS CYS CYS SEQRES 44 A 585 LYS ALA ASP ASP LYS GLU THR CYS PHE ALA GLU GLU GLY SEQRES 45 A 585 LYS LYS LEU VAL ALA ALA SER GLN ALA ALA LEU GLY LEU HELIX 1 AA1 SER A 5 GLY A 15 1 11 HELIX 2 AA2 GLY A 15 LEU A 31 1 17 HELIX 3 AA3 PRO A 35 ASP A 56 1 22 HELIX 4 AA4 ALA A 59 LYS A 64 1 6 HELIX 5 AA5 SER A 65 CYS A 75 1 11 HELIX 6 AA6 TYR A 84 ALA A 92 1 9 HELIX 7 AA7 PRO A 96 HIS A 105 1 10 HELIX 8 AA8 GLU A 119 ASN A 130 1 12 HELIX 9 AA9 ASN A 130 HIS A 146 1 17 HELIX 10 AB1 TYR A 150 CYS A 169 1 20 HELIX 11 AB2 LYS A 174 LEU A 179 1 6 HELIX 12 AB3 LEU A 179 PHE A 223 1 45 HELIX 13 AB4 GLU A 227 HIS A 247 1 21 HELIX 14 AB5 LEU A 250 ASN A 267 1 18 HELIX 15 AB6 GLN A 268 ILE A 271 5 4 HELIX 16 AB7 SER A 273 GLU A 277 5 5 HELIX 17 AB8 PRO A 282 ALA A 291 1 10 HELIX 18 AB9 ASP A 314 ALA A 322 1 9 HELIX 19 AC1 ALA A 322 HIS A 338 1 17 HELIX 20 AC2 SER A 342 CYS A 360 1 19 HELIX 21 AC3 ASP A 365 ALA A 371 1 7 HELIX 22 AC4 LYS A 372 ASP A 375 5 4 HELIX 23 AC5 GLU A 376 GLN A 397 1 22 HELIX 24 AC6 GLY A 399 VAL A 415 1 17 HELIX 25 AC7 SER A 419 CYS A 438 1 20 HELIX 26 AC8 LYS A 444 LYS A 466 1 23 HELIX 27 AC9 SER A 480 VAL A 482 5 3 HELIX 28 AD1 ASN A 483 LEU A 491 1 9 HELIX 29 AD2 ASN A 503 THR A 508 1 6 HELIX 30 AD3 ALA A 511 LEU A 516 1 6 HELIX 31 AD4 SER A 517 LYS A 536 1 20 HELIX 32 AD5 THR A 540 CYS A 558 1 19 HELIX 33 AD6 ASP A 563 ALA A 581 1 19 SSBOND 1 CYS A 53 CYS A 62 1555 1555 2.03 SSBOND 2 CYS A 75 CYS A 91 1555 1555 2.03 SSBOND 3 CYS A 90 CYS A 101 1555 1555 2.03 SSBOND 4 CYS A 124 CYS A 169 1555 1555 2.04 SSBOND 5 CYS A 168 CYS A 177 1555 1555 2.03 SSBOND 6 CYS A 200 CYS A 246 1555 1555 2.03 SSBOND 7 CYS A 245 CYS A 253 1555 1555 2.02 SSBOND 8 CYS A 265 CYS A 279 1555 1555 2.04 SSBOND 9 CYS A 278 CYS A 289 1555 1555 2.03 SSBOND 10 CYS A 360 CYS A 369 1555 1555 2.03 SSBOND 11 CYS A 392 CYS A 438 1555 1555 2.03 SSBOND 12 CYS A 437 CYS A 448 1555 1555 2.03 SSBOND 13 CYS A 461 CYS A 477 1555 1555 2.03 SSBOND 14 CYS A 476 CYS A 487 1555 1555 2.03 SSBOND 15 CYS A 514 CYS A 559 1555 1555 2.03 SSBOND 16 CYS A 558 CYS A 567 1555 1555 2.04 CISPEP 1 GLU A 95 PRO A 96 0 1.29 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