HEADER TRANSPORT PROTEIN 08-NOV-23 8X1N TITLE CRYO-EM STRUCTURE OF HUMAN ALPHA-FETOPROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-FETOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ALPHA-1-FETOPROTEIN,ALPHA-FETOGLOBULIN; COMPND 5 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: AFP, HPAFP; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS N-GLYCOSYLATION, FATTY ACIDS, METAL ION, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Z.M.LIU,M.S.LI,C.WU,K.LIU REVDAT 2 16-OCT-24 8X1N 1 REMARK REVDAT 1 15-MAY-24 8X1N 0 JRNL AUTH K.LIU,C.WU,M.ZHU,J.XU,B.LIN,H.LIN,Z.LIU,M.LI JRNL TITL STRUCTURAL CHARACTERISTICS OF ALPHA-FETOPROTEIN, INCLUDING JRNL TITL 2 N-GLYCOSYLATION, METAL ION AND FATTY ACID BINDING SITES. JRNL REF COMMUN BIOL V. 7 505 2024 JRNL REFN ESSN 2399-3642 JRNL PMID 38678117 JRNL DOI 10.1038/S42003-024-06219-0 REMARK 2 REMARK 2 RESOLUTION. 3.31 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) : 3.310 REMARK 3 NUMBER OF PARTICLES : 144221 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 8X1N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 09-NOV-23. REMARK 100 THE DEPOSITION ID IS D_1300042450. 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 : CRYO-EM STRUCTURE OF HUMAN REMARK 245 ALPHA-FETOPROTEIN 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 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) : 5000.00 REMARK 245 ILLUMINATION MODE : SPOT SCAN 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 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 LYS A 2 REMARK 465 TRP A 3 REMARK 465 VAL A 4 REMARK 465 GLU A 5 REMARK 465 SER A 6 REMARK 465 ILE A 7 REMARK 465 PHE A 8 REMARK 465 LEU A 9 REMARK 465 ILE A 10 REMARK 465 PHE A 11 REMARK 465 LEU A 12 REMARK 465 LEU A 13 REMARK 465 ASN A 14 REMARK 465 PHE A 15 REMARK 465 THR A 16 REMARK 465 GLU A 17 REMARK 465 SER A 18 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 472 CA - CB - SG ANGL. DEV. = 7.3 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 CYS A 113 -166.38 -126.77 REMARK 500 ALA A 134 60.42 62.04 REMARK 500 PHE A 139 109.91 -58.21 REMARK 500 PRO A 144 2.61 -61.37 REMARK 500 ASP A 154 118.55 -161.08 REMARK 500 PHE A 385 49.26 -79.93 REMARK 500 GLN A 386 11.69 -140.41 REMARK 500 CYS A 461 29.66 -142.74 REMARK 500 VAL A 493 -62.98 -100.65 REMARK 500 LYS A 560 82.27 -153.50 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 ZN A 701 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 22 NE2 REMARK 620 2 HIS A 264 NE2 93.5 REMARK 620 3 HIS A 268 NE2 133.7 69.8 REMARK 620 4 ASP A 280 OD2 114.7 107.1 111.5 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-37997 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF HUMAN ALPHA-FETOPROTEIN DBREF 8X1N A 1 609 UNP P02771 FETA_HUMAN 1 609 SEQRES 1 A 609 MET LYS TRP VAL GLU SER ILE PHE LEU ILE PHE LEU LEU SEQRES 2 A 609 ASN PHE THR GLU SER ARG THR LEU HIS ARG ASN GLU TYR SEQRES 3 A 609 GLY ILE ALA SER ILE LEU ASP SER TYR GLN CYS THR ALA SEQRES 4 A 609 GLU ILE SER LEU ALA ASP LEU ALA THR ILE PHE PHE ALA SEQRES 5 A 609 GLN PHE VAL GLN GLU ALA THR TYR LYS GLU VAL SER LYS SEQRES 6 A 609 MET VAL LYS ASP ALA LEU THR ALA ILE GLU LYS PRO THR SEQRES 7 A 609 GLY ASP GLU GLN SER SER GLY CYS LEU GLU ASN GLN LEU SEQRES 8 A 609 PRO ALA PHE LEU GLU GLU LEU CYS HIS GLU LYS GLU ILE SEQRES 9 A 609 LEU GLU LYS TYR GLY HIS SER ASP CYS CYS SER GLN SER SEQRES 10 A 609 GLU GLU GLY ARG HIS ASN CYS PHE LEU ALA HIS LYS LYS SEQRES 11 A 609 PRO THR PRO ALA SER ILE PRO LEU PHE GLN VAL PRO GLU SEQRES 12 A 609 PRO VAL THR SER CYS GLU ALA TYR GLU GLU ASP ARG GLU SEQRES 13 A 609 THR PHE MET ASN LYS PHE ILE TYR GLU ILE ALA ARG ARG SEQRES 14 A 609 HIS PRO PHE LEU TYR ALA PRO THR ILE LEU LEU TRP ALA SEQRES 15 A 609 ALA ARG TYR ASP LYS ILE ILE PRO SER CYS CYS LYS ALA SEQRES 16 A 609 GLU ASN ALA VAL GLU CYS PHE GLN THR LYS ALA ALA THR SEQRES 17 A 609 VAL THR LYS GLU LEU ARG GLU SER SER LEU LEU ASN GLN SEQRES 18 A 609 HIS ALA CYS ALA VAL MET LYS ASN PHE GLY THR ARG THR SEQRES 19 A 609 PHE GLN ALA ILE THR VAL THR LYS LEU SER GLN LYS PHE SEQRES 20 A 609 THR LYS VAL ASN PHE THR GLU ILE GLN LYS LEU VAL LEU SEQRES 21 A 609 ASP VAL ALA HIS VAL HIS GLU HIS CYS CYS ARG GLY ASP SEQRES 22 A 609 VAL LEU ASP CYS LEU GLN ASP GLY GLU LYS ILE MET SER SEQRES 23 A 609 TYR ILE CYS SER GLN GLN ASP THR LEU SER ASN LYS ILE SEQRES 24 A 609 THR GLU CYS CYS LYS LEU THR THR LEU GLU ARG GLY GLN SEQRES 25 A 609 CYS ILE ILE HIS ALA GLU ASN ASP GLU LYS PRO GLU GLY SEQRES 26 A 609 LEU SER PRO ASN LEU ASN ARG PHE LEU GLY ASP ARG ASP SEQRES 27 A 609 PHE ASN GLN PHE SER SER GLY GLU LYS ASN ILE PHE LEU SEQRES 28 A 609 ALA SER PHE VAL HIS GLU TYR SER ARG ARG HIS PRO GLN SEQRES 29 A 609 LEU ALA VAL SER VAL ILE LEU ARG VAL ALA LYS GLY TYR SEQRES 30 A 609 GLN GLU LEU LEU GLU LYS CYS PHE GLN THR GLU ASN PRO SEQRES 31 A 609 LEU GLU CYS GLN ASP LYS GLY GLU GLU GLU LEU GLN LYS SEQRES 32 A 609 TYR ILE GLN GLU SER GLN ALA LEU ALA LYS ARG SER CYS SEQRES 33 A 609 GLY LEU PHE GLN LYS LEU GLY GLU TYR TYR LEU GLN ASN SEQRES 34 A 609 ALA PHE LEU VAL ALA TYR THR LYS LYS ALA PRO GLN LEU SEQRES 35 A 609 THR SER SER GLU LEU MET ALA ILE THR ARG LYS MET ALA SEQRES 36 A 609 ALA THR ALA ALA THR CYS CYS GLN LEU SER GLU ASP LYS SEQRES 37 A 609 LEU LEU ALA CYS GLY GLU GLY ALA ALA ASP ILE ILE ILE SEQRES 38 A 609 GLY HIS LEU CYS ILE ARG HIS GLU MET THR PRO VAL ASN SEQRES 39 A 609 PRO GLY VAL GLY GLN CYS CYS THR SER SER TYR ALA ASN SEQRES 40 A 609 ARG ARG PRO CYS PHE SER SER LEU VAL VAL ASP GLU THR SEQRES 41 A 609 TYR VAL PRO PRO ALA PHE SER ASP ASP LYS PHE ILE PHE SEQRES 42 A 609 HIS LYS ASP LEU CYS GLN ALA GLN GLY VAL ALA LEU GLN SEQRES 43 A 609 THR MET LYS GLN GLU PHE LEU ILE ASN LEU VAL LYS GLN SEQRES 44 A 609 LYS PRO GLN ILE THR GLU GLU GLN LEU GLU ALA VAL ILE SEQRES 45 A 609 ALA ASP PHE SER GLY LEU LEU GLU LYS CYS CYS GLN GLY SEQRES 46 A 609 GLN GLU GLN GLU VAL CYS PHE ALA GLU GLU GLY GLN LYS SEQRES 47 A 609 LEU ILE SER LYS THR ARG ALA ALA LEU GLY VAL HET NAG B 1 14 HET NAG B 2 14 HET BMA B 3 11 HET ZN A 701 1 HET PLM A 702 18 HET PLM A 703 18 HET PLM A 704 18 HET PLM A 705 18 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM ZN ZINC ION HETNAM PLM PALMITIC ACID HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 2 NAG 2(C8 H15 N O6) FORMUL 2 BMA C6 H12 O6 FORMUL 3 ZN ZN 2+ FORMUL 4 PLM 4(C16 H32 O2) HELIX 1 AA1 SER A 42 VAL A 55 1 14 HELIX 2 AA2 THR A 59 GLU A 75 1 17 HELIX 3 AA3 GLN A 90 CYS A 99 1 10 HELIX 4 AA4 GLU A 101 TYR A 108 1 8 HELIX 5 AA5 SER A 117 HIS A 128 1 12 HELIX 6 AA6 THR A 146 ASP A 154 1 9 HELIX 7 AA7 ASP A 154 HIS A 170 1 17 HELIX 8 AA8 TYR A 174 CYS A 193 1 20 HELIX 9 AA9 ASN A 197 PHE A 247 1 51 HELIX 10 AB1 ASN A 251 ARG A 271 1 21 HELIX 11 AB2 ASP A 273 GLN A 291 1 19 HELIX 12 AB3 SER A 296 CYS A 303 1 8 HELIX 13 AB4 THR A 306 ALA A 317 1 12 HELIX 14 AB5 SER A 343 HIS A 362 1 20 HELIX 15 AB6 ALA A 366 PHE A 385 1 20 HELIX 16 AB7 ASN A 389 LEU A 401 1 13 HELIX 17 AB8 GLN A 402 GLY A 423 1 22 HELIX 18 AB9 GLY A 423 ALA A 439 1 17 HELIX 19 AC1 THR A 443 CYS A 462 1 20 HELIX 20 AC2 ASP A 467 THR A 491 1 25 HELIX 21 AC3 ASN A 494 THR A 502 1 9 HELIX 22 AC4 ASN A 507 SER A 513 1 7 HELIX 23 AC5 SER A 527 ILE A 532 5 6 HELIX 24 AC6 LYS A 535 ALA A 540 1 6 HELIX 25 AC7 GLY A 542 LYS A 560 1 19 HELIX 26 AC8 THR A 564 GLN A 584 1 21 HELIX 27 AC9 GLU A 587 GLY A 608 1 22 SSBOND 1 CYS A 37 CYS A 86 1555 1555 2.03 SSBOND 2 CYS A 99 CYS A 114 1555 1555 2.03 SSBOND 3 CYS A 113 CYS A 124 1555 1555 2.03 SSBOND 4 CYS A 148 CYS A 193 1555 1555 2.04 SSBOND 5 CYS A 192 CYS A 201 1555 1555 2.04 SSBOND 6 CYS A 224 CYS A 270 1555 1555 2.04 SSBOND 7 CYS A 269 CYS A 277 1555 1555 2.03 SSBOND 8 CYS A 289 CYS A 303 1555 1555 2.03 SSBOND 9 CYS A 302 CYS A 313 1555 1555 2.03 SSBOND 10 CYS A 384 CYS A 393 1555 1555 2.04 SSBOND 11 CYS A 416 CYS A 462 1555 1555 2.04 SSBOND 12 CYS A 461 CYS A 472 1555 1555 2.03 SSBOND 13 CYS A 485 CYS A 501 1555 1555 2.03 SSBOND 14 CYS A 500 CYS A 511 1555 1555 2.03 SSBOND 15 CYS A 538 CYS A 583 1555 1555 2.03 SSBOND 16 CYS A 582 CYS A 591 1555 1555 2.03 LINK ND2 ASN A 251 C1 NAG B 1 1555 1555 1.45 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.44 LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.44 LINK NE2 HIS A 22 ZN ZN A 701 1555 1555 2.41 LINK NE2 HIS A 264 ZN ZN A 701 1555 1555 2.35 LINK NE2 HIS A 268 ZN ZN A 701 1555 1555 2.30 LINK OD2 ASP A 280 ZN ZN A 701 1555 1555 2.45 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