HEADER OXYGEN TRANSPORT 14-NOV-16 5ME2 OBSLTE 26-JUL-17 5ME2 5NI1 TITLE CRYOEM STRUCTURE OF HAEMOGLOBIN AT 3.2 A DETERMINED WITH THE VOLTA TITLE 2 PHASE PLATE 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 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HEMOGLOBIN SUBUNIT BETA; COMPND 8 CHAIN: B, D; COMPND 9 SYNONYM: BETA-GLOBIN,HEMOGLOBIN BETA CHAIN; COMPND 10 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: HBA1, HBA2; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: HBB; SOURCE 14 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 15 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS VOLTA PHASE PLATE, SINGLE PARTICLE ANALYSIS, HEMOGLOBIN, OXYGEN KEYWDS 2 TRANSPORT EXPDTA ELECTRON MICROSCOPY AUTHOR M.KHOSHOUEI,M.RADJAINIA,W.BAUMEISTER,R.DANEV REVDAT 2 26-JUL-17 5ME2 1 REVDAT 1 23-NOV-16 5ME2 0 JRNL AUTH M.KHOSHOUEI,M.RADJAINIA,W.BAUMEISTER,R.DANEV JRNL TITL CRYO-EM STRUCTURE OF HAEMOGLOBIN AT 3.2 A DETERMINED WITH JRNL TITL 2 THE VOLTA PHASE PLATE JRNL REF BIORXIV 2016 JRNL REFN JRNL DOI 10.1101/087841 REMARK 2 REMARK 2 RESOLUTION. 3.20 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) : 3.200 REMARK 3 NUMBER OF PARTICLES : 175300 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 5ME2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-NOV-16. REMARK 100 THE DEPOSITION ID IS D_1200002319. 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 : HEMOGLOBIN 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 K2 SUMMIT (4K X 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) : 40.00 REMARK 245 ILLUMINATION MODE : OTHER 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -108.0 KCAL/MOL 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 PHE A 46 162.84 176.24 REMARK 500 HIS A 89 -69.10 -91.28 REMARK 500 SER A 138 163.59 175.30 REMARK 500 LYS B 95 -62.86 -109.15 REMARK 500 PHE C 46 162.85 176.29 REMARK 500 HIS C 89 -69.09 -91.33 REMARK 500 SER C 138 163.58 175.34 REMARK 500 LYS D 95 -63.70 -107.01 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 85.8 REMARK 620 3 HEM A 201 NB 92.5 91.3 REMARK 620 4 HEM A 201 NC 92.7 178.5 89.0 REMARK 620 5 HEM A 201 ND 88.2 88.6 179.3 91.1 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 87.4 REMARK 620 3 HEM B 201 NB 103.7 90.4 REMARK 620 4 HEM B 201 NC 97.4 175.0 89.7 REMARK 620 5 HEM B 201 ND 78.9 89.9 177.4 89.8 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 91.7 REMARK 620 3 HEM C 201 NB 90.8 89.3 REMARK 620 4 HEM C 201 NC 88.8 179.2 90.1 REMARK 620 5 HEM C 201 ND 88.5 90.7 179.4 89.9 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 79.4 REMARK 620 3 HEM D 201 NB 100.9 89.9 REMARK 620 4 HEM D 201 NC 103.7 177.0 89.9 REMARK 620 5 HEM D 201 ND 85.4 90.0 173.6 89.8 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-3488 RELATED DB: EMDB DBREF 5ME2 A 1 140 UNP P69905 HBA_HUMAN 2 141 DBREF 5ME2 B 1 143 UNP P68871 HBB_HUMAN 2 144 DBREF 5ME2 C 1 140 UNP P69905 HBA_HUMAN 2 141 DBREF 5ME2 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 LYS A 7 TRP A 14 1 8 HELIX 2 AA2 VAL A 17 ALA A 19 5 3 HELIX 3 AA3 HIS A 20 PHE A 36 1 17 HELIX 4 AA4 PRO A 37 PHE A 43 5 7 HELIX 5 AA5 SER A 52 HIS A 72 1 21 HELIX 6 AA6 ASP A 75 LEU A 80 1 6 HELIX 7 AA7 LEU A 80 HIS A 89 1 10 HELIX 8 AA8 ASP A 94 LEU A 113 1 20 HELIX 9 AA9 PRO A 114 PHE A 117 5 4 HELIX 10 AB1 THR A 118 THR A 137 1 20 HELIX 11 AB2 THR B 4 LYS B 17 1 14 HELIX 12 AB3 GLU B 22 TYR B 35 1 14 HELIX 13 AB4 THR B 38 GLU B 43 1 6 HELIX 14 AB5 SER B 44 GLY B 46 5 3 HELIX 15 AB6 THR B 50 GLY B 56 1 7 HELIX 16 AB7 ASN B 57 HIS B 77 1 21 HELIX 17 AB8 ASN B 80 PHE B 85 1 6 HELIX 18 AB9 PHE B 85 LYS B 95 1 11 HELIX 19 AC1 GLU B 101 GLY B 119 1 19 HELIX 20 AC2 LYS B 120 PHE B 122 5 3 HELIX 21 AC3 THR B 123 LEU B 141 1 19 HELIX 22 AC4 LYS C 7 TRP C 14 1 8 HELIX 23 AC5 VAL C 17 ALA C 19 5 3 HELIX 24 AC6 HIS C 20 PHE C 36 1 17 HELIX 25 AC7 PRO C 37 PHE C 43 5 7 HELIX 26 AC8 SER C 52 HIS C 72 1 21 HELIX 27 AC9 ASP C 75 LEU C 80 1 6 HELIX 28 AD1 LEU C 80 HIS C 89 1 10 HELIX 29 AD2 ASP C 94 LEU C 113 1 20 HELIX 30 AD3 PRO C 114 PHE C 117 5 4 HELIX 31 AD4 THR C 118 THR C 137 1 20 HELIX 32 AD5 THR D 4 LYS D 17 1 14 HELIX 33 AD6 GLU D 22 TYR D 35 1 14 HELIX 34 AD7 THR D 38 GLU D 43 1 6 HELIX 35 AD8 SER D 44 GLY D 46 5 3 HELIX 36 AD9 THR D 50 GLY D 56 1 7 HELIX 37 AE1 ASN D 57 HIS D 77 1 21 HELIX 38 AE2 ASN D 80 PHE D 85 1 6 HELIX 39 AE3 PHE D 85 LYS D 95 1 11 HELIX 40 AE4 GLU D 101 GLY D 119 1 19 HELIX 41 AE5 LYS D 120 PHE D 122 5 3 HELIX 42 AE6 THR D 123 LEU D 141 1 19 LINK NE2 HIS A 87 FE HEM A 201 1555 1555 2.66 LINK NE2 HIS B 92 FE HEM B 201 1555 1555 2.74 LINK NE2 HIS C 87 FE HEM C 201 1555 1555 2.65 LINK NE2 HIS D 92 FE HEM D 201 1555 1555 2.75 SITE 1 AC1 9 TYR A 42 PHE A 43 HIS A 58 LEU A 86 SITE 2 AC1 9 HIS A 87 LEU A 91 ASN A 97 PHE A 98 SITE 3 AC1 9 LEU A 101 SITE 1 AC2 8 LEU B 31 PHE B 42 LYS B 66 HIS B 92 SITE 2 AC2 8 ASN B 102 LEU B 106 VAL B 137 LEU B 141 SITE 1 AC3 10 TYR C 42 PHE C 43 LYS C 61 LEU C 66 SITE 2 AC3 10 LEU C 83 HIS C 87 LEU C 91 ASN C 97 SITE 3 AC3 10 PHE C 98 VAL C 132 SITE 1 AC4 9 THR D 38 PHE D 41 PHE D 42 PHE D 45 SITE 2 AC4 9 LYS D 66 HIS D 92 ASN D 102 LEU D 106 SITE 3 AC4 9 LEU D 141 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 2 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 0.009524 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009524 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009524 0.00000