HEADER OXYGEN TRANSPORT 06-DEC-18 6NBC TITLE HUMAN METHEMOGLOBIN STATE 1 DETERMINED USING SINGLE-PARTICLE CRYO-EM TITLE 2 AT 200 KEV COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMOGLOBIN SUBUNIT ALPHA; COMPND 3 CHAIN: A, C; COMPND 4 SYNONYM: ALPHA-GLOBIN,HEMOGLOBIN ALPHA CHAIN; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HEMOGLOBIN SUBUNIT BETA; COMPND 7 CHAIN: B, D; COMPND 8 SYNONYM: BETA-GLOBIN,HEMOGLOBIN BETA CHAIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606 KEYWDS HEME-BINDING, HETERO-4-MER, GLOBIN, OXYGEN TRANSPORT EXPDTA ELECTRON MICROSCOPY NUMMDL 10 AUTHOR M.A.HERZIK JR.,M.WU,G.C.LANDER REVDAT 4 20-MAR-24 6NBC 1 REMARK REVDAT 3 18-DEC-19 6NBC 1 SCALE REVDAT 2 20-MAR-19 6NBC 1 JRNL REVDAT 1 13-MAR-19 6NBC 0 JRNL AUTH M.A.HERZIK JR.,M.WU,G.C.LANDER JRNL TITL HIGH-RESOLUTION STRUCTURE DETERMINATION OF SUB-100 KDA JRNL TITL 2 COMPLEXES USING CONVENTIONAL CRYO-EM. JRNL REF NAT COMMUN V. 10 1032 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 30833564 JRNL DOI 10.1038/S41467-019-08991-8 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, LEGINON, CTFFIND, UCSF CHIMERA, REMARK 3 RELION, RELION, RELION, RELION, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 4N7P REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : 67.000 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) : 2.800 REMARK 3 NUMBER OF PARTICLES : 24308 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 6NBC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-DEC-18. REMARK 100 THE DEPOSITION ID IS D_1000238401. 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 : METHEMOGLOBIN FROM HUMAN REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 12.00 REMARK 245 SAMPLE SUPPORT DETAILS : GRIDS WERE PLASMA CLEANED USING REMARK 245 A SOLARUS PLASMA CLEANER (GATAN, REMARK 245 INC.). REMARK 245 SAMPLE VITRIFICATION DETAILS : SAMPLE WAS MANUALLY BLOTTED FOR REMARK 245 4-5 SECONDS USING WHATMAN NO. 1 REMARK 245 FILTER PAPER IMMEDIATELY PRIOR REMARK 245 TO PLUNGE-FREEZING. REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : LYOPHILIZED HUMAN METHEMOGLOBIN REMARK 245 PURCHASED FROM SIGMA ALDRICH REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 1673 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TALOS ARCTICA REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 5000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 16000.00 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) : 6900.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 73000 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 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 4 LEU A 80 30.31 -98.08 REMARK 500 5 LEU C 80 30.00 -96.60 REMARK 500 5 PHE D 85 41.22 -109.34 REMARK 500 5 LYS D 95 -35.53 -131.35 REMARK 500 8 LEU C 80 31.36 -96.70 REMARK 500 10 LEU A 80 30.36 -95.48 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 HEM A 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 87 NE2 REMARK 620 2 HEM A 201 NA 82.8 REMARK 620 3 HEM A 201 NB 91.1 90.2 REMARK 620 4 HEM A 201 NC 92.6 175.4 90.6 REMARK 620 5 HEM A 201 ND 87.9 90.2 179.0 88.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 92 NE2 REMARK 620 2 HEM B 201 NA 82.2 REMARK 620 3 HEM B 201 NB 96.8 90.0 REMARK 620 4 HEM B 201 NC 93.7 175.9 90.4 REMARK 620 5 HEM B 201 ND 79.8 89.7 176.6 89.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM C 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 87 NE2 REMARK 620 2 HEM C 201 NA 82.2 REMARK 620 3 HEM C 201 NB 89.8 88.3 REMARK 620 4 HEM C 201 NC 92.7 174.9 91.7 REMARK 620 5 HEM C 201 ND 88.5 91.5 178.3 88.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM D 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS D 92 NE2 REMARK 620 2 HEM D 201 NA 77.8 REMARK 620 3 HEM D 201 NB 95.3 87.7 REMARK 620 4 HEM D 201 NC 96.1 173.8 91.6 REMARK 620 5 HEM D 201 ND 82.2 91.9 177.5 88.6 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM D 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-0407 RELATED DB: EMDB REMARK 900 HUMAN METHEMOGLOBIN STATE 1 DETERMINED USING SINGLE-PARTICLE CRYO- REMARK 900 EM AT 200 KEV DBREF 6NBC A 1 140 UNP P69905 HBA_HUMAN 2 141 DBREF 6NBC B 1 143 UNP P68871 HBB_HUMAN 2 144 DBREF 6NBC C 1 140 UNP P69905 HBA_HUMAN 2 141 DBREF 6NBC D 1 143 UNP P68871 HBB_HUMAN 2 144 SEQRES 1 A 140 VAL LEU SER PRO ALA ASP LYS THR ASN VAL LYS ALA ALA SEQRES 2 A 140 TRP GLY LYS VAL GLY ALA HIS ALA GLY GLU TYR GLY ALA SEQRES 3 A 140 GLU ALA LEU GLU ARG MET PHE LEU SER PHE PRO THR THR SEQRES 4 A 140 LYS THR TYR PHE PRO HIS PHE ASP LEU SER HIS GLY SER SEQRES 5 A 140 ALA GLN VAL LYS GLY HIS GLY LYS LYS VAL ALA ASP ALA SEQRES 6 A 140 LEU THR ASN ALA VAL ALA HIS VAL ASP ASP MET PRO ASN SEQRES 7 A 140 ALA LEU SER ALA LEU SER ASP LEU HIS ALA HIS LYS LEU SEQRES 8 A 140 ARG VAL ASP PRO VAL ASN PHE LYS LEU LEU SER HIS CYS SEQRES 9 A 140 LEU LEU VAL THR LEU ALA ALA HIS LEU PRO ALA GLU PHE SEQRES 10 A 140 THR PRO ALA VAL HIS ALA SER LEU ASP LYS PHE LEU ALA SEQRES 11 A 140 SER VAL SER THR VAL LEU THR SER LYS TYR SEQRES 1 B 143 VAL HIS LEU THR PRO GLU GLU LYS SER ALA VAL THR ALA SEQRES 2 B 143 LEU TRP GLY LYS VAL ASN VAL ASP GLU VAL GLY GLY GLU SEQRES 3 B 143 ALA LEU GLY ARG LEU LEU VAL VAL TYR PRO TRP THR GLN SEQRES 4 B 143 ARG PHE PHE GLU SER PHE GLY ASP LEU SER THR PRO ASP SEQRES 5 B 143 ALA VAL MET GLY ASN PRO LYS VAL LYS ALA HIS GLY LYS SEQRES 6 B 143 LYS VAL LEU GLY ALA PHE SER ASP GLY LEU ALA HIS LEU SEQRES 7 B 143 ASP ASN LEU LYS GLY THR PHE ALA THR LEU SER GLU LEU SEQRES 8 B 143 HIS CYS ASP LYS LEU HIS VAL ASP PRO GLU ASN PHE ARG SEQRES 9 B 143 LEU LEU GLY ASN VAL LEU VAL CYS VAL LEU ALA HIS HIS SEQRES 10 B 143 PHE GLY LYS GLU PHE THR PRO PRO VAL GLN ALA ALA TYR SEQRES 11 B 143 GLN LYS VAL VAL ALA GLY VAL ALA ASN ALA LEU ALA HIS SEQRES 1 C 140 VAL LEU SER PRO ALA ASP LYS THR ASN VAL LYS ALA ALA SEQRES 2 C 140 TRP GLY LYS VAL GLY ALA HIS ALA GLY GLU TYR GLY ALA SEQRES 3 C 140 GLU ALA LEU GLU ARG MET PHE LEU SER PHE PRO THR THR SEQRES 4 C 140 LYS THR TYR PHE PRO HIS PHE ASP LEU SER HIS GLY SER SEQRES 5 C 140 ALA GLN VAL LYS GLY HIS GLY LYS LYS VAL ALA ASP ALA SEQRES 6 C 140 LEU THR ASN ALA VAL ALA HIS VAL ASP ASP MET PRO ASN SEQRES 7 C 140 ALA LEU SER ALA LEU SER ASP LEU HIS ALA HIS LYS LEU SEQRES 8 C 140 ARG VAL ASP PRO VAL ASN PHE LYS LEU LEU SER HIS CYS SEQRES 9 C 140 LEU LEU VAL THR LEU ALA ALA HIS LEU PRO ALA GLU PHE SEQRES 10 C 140 THR PRO ALA VAL HIS ALA SER LEU ASP LYS PHE LEU ALA SEQRES 11 C 140 SER VAL SER THR VAL LEU THR SER LYS TYR SEQRES 1 D 143 VAL HIS LEU THR PRO GLU GLU LYS SER ALA VAL THR ALA SEQRES 2 D 143 LEU TRP GLY LYS VAL ASN VAL ASP GLU VAL GLY GLY GLU SEQRES 3 D 143 ALA LEU GLY ARG LEU LEU VAL VAL TYR PRO TRP THR GLN SEQRES 4 D 143 ARG PHE PHE GLU SER PHE GLY ASP LEU SER THR PRO ASP SEQRES 5 D 143 ALA VAL MET GLY ASN PRO LYS VAL LYS ALA HIS GLY LYS SEQRES 6 D 143 LYS VAL LEU GLY ALA PHE SER ASP GLY LEU ALA HIS LEU SEQRES 7 D 143 ASP ASN LEU LYS GLY THR PHE ALA THR LEU SER GLU LEU SEQRES 8 D 143 HIS CYS ASP LYS LEU HIS VAL ASP PRO GLU ASN PHE ARG SEQRES 9 D 143 LEU LEU GLY ASN VAL LEU VAL CYS VAL LEU ALA HIS HIS SEQRES 10 D 143 PHE GLY LYS GLU PHE THR PRO PRO VAL GLN ALA ALA TYR SEQRES 11 D 143 GLN LYS VAL VAL ALA GLY VAL ALA ASN ALA LEU ALA HIS HET HEM A 201 43 HET HEM B 201 43 HET HEM C 201 43 HET HEM D 201 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 5 HEM 4(C34 H32 FE N4 O4) HELIX 1 AA1 SER A 3 GLY A 18 1 16 HELIX 2 AA2 HIS A 20 PHE A 36 1 17 HELIX 3 AA3 PRO A 37 PHE A 43 5 7 HELIX 4 AA4 SER A 52 HIS A 72 1 21 HELIX 5 AA5 ASP A 75 LEU A 80 1 6 HELIX 6 AA6 LEU A 80 ALA A 88 1 9 HELIX 7 AA7 ASP A 94 LEU A 113 1 20 HELIX 8 AA8 THR A 118 SER A 138 1 21 HELIX 9 AA9 THR B 4 GLY B 16 1 13 HELIX 10 AB1 ASN B 19 TYR B 35 1 17 HELIX 11 AB2 PRO B 36 GLY B 46 5 11 HELIX 12 AB3 THR B 50 MET B 55 1 6 HELIX 13 AB4 ASN B 57 ALA B 76 1 20 HELIX 14 AB5 ASN B 80 PHE B 85 1 6 HELIX 15 AB6 PHE B 85 ASP B 94 1 10 HELIX 16 AB7 ASP B 99 GLY B 119 1 21 HELIX 17 AB8 LYS B 120 PHE B 122 5 3 HELIX 18 AB9 THR B 123 ALA B 142 1 20 HELIX 19 AC1 SER C 3 GLY C 18 1 16 HELIX 20 AC2 HIS C 20 PHE C 36 1 17 HELIX 21 AC3 PRO C 37 PHE C 43 5 7 HELIX 22 AC4 SER C 52 HIS C 72 1 21 HELIX 23 AC5 ASP C 75 LEU C 80 1 6 HELIX 24 AC6 LEU C 80 ALA C 88 1 9 HELIX 25 AC7 ASP C 94 LEU C 113 1 20 HELIX 26 AC8 THR C 118 THR C 137 1 20 HELIX 27 AC9 THR D 4 GLY D 16 1 13 HELIX 28 AD1 ASN D 19 TYR D 35 1 17 HELIX 29 AD2 PRO D 36 GLY D 46 5 11 HELIX 30 AD3 THR D 50 MET D 55 1 6 HELIX 31 AD4 ASN D 57 ALA D 76 1 20 HELIX 32 AD5 ASN D 80 PHE D 85 1 6 HELIX 33 AD6 ALA D 86 ASP D 94 1 9 HELIX 34 AD7 ASP D 99 GLY D 119 1 21 HELIX 35 AD8 LYS D 120 PHE D 122 5 3 HELIX 36 AD9 THR D 123 ALA D 142 1 20 LINK NE2 HIS A 87 FE HEM A 201 1555 1555 2.07 LINK NE2 HIS B 92 FE HEM B 201 1555 1555 2.15 LINK NE2 HIS C 87 FE HEM C 201 1555 1555 2.08 LINK NE2 HIS D 92 FE HEM D 201 1555 1555 2.18 SITE 1 AC1 13 TYR A 42 PHE A 43 HIS A 45 PHE A 46 SITE 2 AC1 13 HIS A 58 LYS A 61 LEU A 86 HIS A 87 SITE 3 AC1 13 LEU A 91 VAL A 93 ASN A 97 PHE A 98 SITE 4 AC1 13 LEU A 101 SITE 1 AC2 13 THR B 38 PHE B 41 PHE B 42 PHE B 45 SITE 2 AC2 13 HIS B 63 LYS B 66 LEU B 88 HIS B 92 SITE 3 AC2 13 LEU B 96 ASN B 102 PHE B 103 LEU B 106 SITE 4 AC2 13 LEU B 141 SITE 1 AC3 12 TYR C 42 PHE C 43 HIS C 45 PHE C 46 SITE 2 AC3 12 HIS C 58 LYS C 61 LEU C 86 HIS C 87 SITE 3 AC3 12 LEU C 91 ASN C 97 PHE C 98 LEU C 101 SITE 1 AC4 13 THR D 38 PHE D 41 PHE D 42 PHE D 45 SITE 2 AC4 13 HIS D 63 LYS D 66 PHE D 71 HIS D 92 SITE 3 AC4 13 LEU D 96 ASN D 102 PHE D 103 LEU D 106 SITE 4 AC4 13 LEU D 141 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 MODEL 1