HEADER OXYGEN BINDING 25-SEP-23 8WJ1 TITLE CRYO-EM STRUCTURE OF HUMAN HAEMOGLOBIN IN OXY FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMOGLOBIN SUBUNIT ALPHA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ALPHA-GLOBIN,HEMOGLOBIN ALPHA CHAIN; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HEMOGLOBIN SUBUNIT BETA; COMPND 7 CHAIN: B; 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 HAEMOGLOBIN, OXYGEN BINDING EXPDTA ELECTRON MICROSCOPY AUTHOR K.TAKAHASHI,Y.LEE,A.FAGO,N.M.BAUTISTA,A.KAWAMOTO,G.KURISU,J.STORZ, AUTHOR 2 T.NISHIZAWA,J.R.H.TAME REVDAT 1 14-AUG-24 8WJ1 0 JRNL AUTH K.TAKAHASHI,Y.LEE,A.FAGO,N.M.BAUTISTA,J.F.STORZ,A.KAWAMOTO, JRNL AUTH 2 G.KURISU,T.NISHIZAWA,J.R.H.TAME JRNL TITL THE UNIQUE ALLOSTERIC PROPERTY OF CROCODILIAN HAEMOGLOBIN JRNL TITL 2 ELUCIDATED BY CRYO-EM. JRNL REF NAT COMMUN V. 15 6505 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 39090102 JRNL DOI 10.1038/S41467-024-49947-X REMARK 2 REMARK 2 RESOLUTION. 2.27 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EPU, CRYOSPARC, COOT, ISOLDE, UCSF REMARK 3 CHIMERAX, SERVALCAT, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 2DN1 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) : 2.270 REMARK 3 NUMBER OF PARTICLES : 550843 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 8WJ1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1300041361. 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 HAEMOGLOBIN IN OXY FORM 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 : 7.50 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) : 400.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1200.00 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) : 6000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 165000 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 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 261.12000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 261.12000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 261.12000 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 261.12000 REMARK 350 BIOMT3 3 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 0 REMARK 465 MET B 0 REMARK 465 VAL B 1 REMARK 465 LYS B 144 REMARK 465 TYR B 145 REMARK 465 HIS B 146 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 OE1 GLU A 116 O HOH A 301 2.19 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 ARG B 30 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG B 30 NE - CZ - NH2 ANGL. DEV. = 3.4 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 TYR B 35 74.77 -119.53 REMARK 500 ASN B 80 45.10 101.39 REMARK 500 CYS B 93 -65.69 -101.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 92 0.15 SIDE CHAIN REMARK 500 ARG B 30 0.25 SIDE CHAIN REMARK 500 ARG B 104 0.13 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 366 DISTANCE = 6.14 ANGSTROMS 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 87.0 REMARK 620 3 HEM A 201 NB 87.3 86.2 REMARK 620 4 HEM A 201 NC 94.6 175.0 89.2 REMARK 620 5 HEM A 201 ND 97.2 92.7 175.3 91.8 REMARK 620 6 OXY A 202 O1 172.3 95.4 85.6 82.5 90.0 REMARK 620 N 1 2 3 4 5 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 90.4 REMARK 620 3 HEM B 201 NB 88.7 85.0 REMARK 620 4 HEM B 201 NC 91.2 174.1 89.4 REMARK 620 5 HEM B 201 ND 95.1 92.6 175.5 92.8 REMARK 620 6 OXY B 202 O1 174.3 93.1 87.1 84.9 89.3 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-37575 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF HUMAN HAEMOGLOBIN IN OXY FORM DBREF 8WJ1 A 0 141 UNP P69905 HBA_HUMAN 1 142 DBREF 8WJ1 B 0 146 UNP P68871 HBB_HUMAN 1 147 SEQRES 1 A 142 MET VAL LEU SER PRO ALA ASP LYS THR ASN VAL LYS ALA SEQRES 2 A 142 ALA TRP GLY LYS VAL GLY ALA HIS ALA GLY GLU TYR GLY SEQRES 3 A 142 ALA GLU ALA LEU GLU ARG MET PHE LEU SER PHE PRO THR SEQRES 4 A 142 THR LYS THR TYR PHE PRO HIS PHE ASP LEU SER HIS GLY SEQRES 5 A 142 SER ALA GLN VAL LYS GLY HIS GLY LYS LYS VAL ALA ASP SEQRES 6 A 142 ALA LEU THR ASN ALA VAL ALA HIS VAL ASP ASP MET PRO SEQRES 7 A 142 ASN ALA LEU SER ALA LEU SER ASP LEU HIS ALA HIS LYS SEQRES 8 A 142 LEU ARG VAL ASP PRO VAL ASN PHE LYS LEU LEU SER HIS SEQRES 9 A 142 CYS LEU LEU VAL THR LEU ALA ALA HIS LEU PRO ALA GLU SEQRES 10 A 142 PHE THR PRO ALA VAL HIS ALA SER LEU ASP LYS PHE LEU SEQRES 11 A 142 ALA SER VAL SER THR VAL LEU THR SER LYS TYR ARG SEQRES 1 B 147 MET VAL HIS LEU THR PRO GLU GLU LYS SER ALA VAL THR SEQRES 2 B 147 ALA LEU TRP GLY LYS VAL ASN VAL ASP GLU VAL GLY GLY SEQRES 3 B 147 GLU ALA LEU GLY ARG LEU LEU VAL VAL TYR PRO TRP THR SEQRES 4 B 147 GLN ARG PHE PHE GLU SER PHE GLY ASP LEU SER THR PRO SEQRES 5 B 147 ASP ALA VAL MET GLY ASN PRO LYS VAL LYS ALA HIS GLY SEQRES 6 B 147 LYS LYS VAL LEU GLY ALA PHE SER ASP GLY LEU ALA HIS SEQRES 7 B 147 LEU ASP ASN LEU LYS GLY THR PHE ALA THR LEU SER GLU SEQRES 8 B 147 LEU HIS CYS ASP LYS LEU HIS VAL ASP PRO GLU ASN PHE SEQRES 9 B 147 ARG LEU LEU GLY ASN VAL LEU VAL CYS VAL LEU ALA HIS SEQRES 10 B 147 HIS PHE GLY LYS GLU PHE THR PRO PRO VAL GLN ALA ALA SEQRES 11 B 147 TYR GLN LYS VAL VAL ALA GLY VAL ALA ASN ALA LEU ALA SEQRES 12 B 147 HIS LYS TYR HIS HET HEM A 201 43 HET OXY A 202 2 HET HEM B 201 43 HET OXY B 202 2 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM OXY OXYGEN MOLECULE HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 4 OXY 2(O2) FORMUL 7 HOH *123(H2 O) 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 HIS A 89 1 10 HELIX 7 AA7 PRO A 95 LEU A 113 1 19 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 GLU B 22 TYR B 35 1 14 HELIX 11 AB2 PRO B 36 GLY B 46 5 11 HELIX 12 AB3 THR B 50 ASN B 57 1 8 HELIX 13 AB4 ASN B 57 ALA B 76 1 20 HELIX 14 AB5 ASN B 80 ASP B 94 1 15 HELIX 15 AB6 PRO B 100 GLY B 119 1 20 HELIX 16 AB7 LYS B 120 PHE B 122 5 3 HELIX 17 AB8 THR B 123 ALA B 142 1 20 LINK NE2 HIS A 87 FE HEM A 201 1555 1555 2.15 LINK FE HEM A 201 O1 OXY A 202 1555 1555 2.05 LINK NE2 HIS B 92 FE HEM B 201 1555 1555 2.11 LINK FE HEM B 201 O1 OXY B 202 1555 1555 1.97 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 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 -1.000000 0.000000 0.000000 261.12000 MTRIX2 2 0.000000 -1.000000 0.000000 261.12000 MTRIX3 2 0.000000 0.000000 1.000000 0.00000