HEADER OXYGEN BINDING 18-JUN-25 9VIC TITLE CRYO-EM STRUCTURE OF HUMAN HAEMOGLOBIN IN THE R CONFORMATION 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,T.NISHIZAWA,J.R.H.TAME REVDAT 1 23-JUL-25 9VIC 0 JRNL AUTH K.TAKAHASHI,Y.LEE,T.NISHIZAWA,J.R.H.TAME JRNL TITL CONFORMATIONAL ANALYSIS OF LIGANDED HUMAN HEMOGLOBIN BY CRYO JRNL TITL 2 ELECTRON MICROSCOPY JRNL REF BIORXIV 2025 JRNL REFN ISSN 2692-8205 JRNL DOI 10.1101/2025.07.07.661630 REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, REFMAC, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 8WJ0 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) : 2.450 REMARK 3 NUMBER OF PARTICLES : 123614 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 9VIC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-JUN-25. REMARK 100 THE DEPOSITION ID IS D_1300060539. 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 CARBOXY REMARK 245 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 : TFS 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) : 5840.00 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 CYCLIC POINT SYMMETRY (SCHOENFLIES SYMBOL = C2). 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 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 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 O VAL A 93 OH TYR A 140 2.07 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 TYR A 42 N - CA - CB ANGL. DEV. = -16.1 DEGREES REMARK 500 ARG A 92 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 141 NE - CZ - NH1 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 LEU A 48 77.84 -111.59 REMARK 500 SER A 138 73.58 -64.69 REMARK 500 LYS A 139 -136.65 -176.69 REMARK 500 TYR A 140 -63.65 124.16 REMARK 500 CYS B 93 -51.98 -127.05 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 0.25 SIDE CHAIN REMARK 500 ARG A 141 0.22 SIDE CHAIN 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 87.5 REMARK 620 3 HEM A 201 NB 85.8 88.6 REMARK 620 4 HEM A 201 NC 89.0 174.8 87.3 REMARK 620 5 HEM A 201 ND 92.7 95.1 176.0 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 90.0 REMARK 620 3 HEM B 201 NB 92.1 85.7 REMARK 620 4 HEM B 201 NC 93.2 173.4 88.5 REMARK 620 5 HEM B 201 ND 91.4 94.2 176.5 91.4 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-65083 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF HUMAN HAEMOGLOBIN IN THE R CONFORMATION DBREF 9VIC A 0 141 UNP P69905 HBA_HUMAN 1 142 DBREF 9VIC 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 CMO A 202 2 HET HEM B 201 43 HET CMO B 202 2 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM CMO CARBON MONOXIDE HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 4 CMO 2(C 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 HIS B 77 1 21 HELIX 14 AB5 ASN B 80 PHE B 85 1 6 HELIX 15 AB6 PHE B 85 HIS B 92 1 8 HELIX 16 AB7 PRO B 100 GLY B 119 1 20 HELIX 17 AB8 LYS B 120 PHE B 122 5 3 HELIX 18 AB9 THR B 123 LEU B 141 1 19 LINK NE2 HIS A 87 FE HEM A 201 1555 1555 2.47 LINK NE2 HIS B 92 FE HEM B 201 1555 1555 2.25 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 CONECT 650 2198 CONECT 1764 2243 CONECT 2156 2160 2187 CONECT 2157 2163 2170 CONECT 2158 2173 2177 CONECT 2159 2180 2184 CONECT 2160 2156 2161 2194 CONECT 2161 2160 2162 2165 CONECT 2162 2161 2163 2164 CONECT 2163 2157 2162 2194 CONECT 2164 2162 CONECT 2165 2161 2166 CONECT 2166 2165 2167 CONECT 2167 2166 2168 2169 CONECT 2168 2167 CONECT 2169 2167 CONECT 2170 2157 2171 2195 CONECT 2171 2170 2172 2174 CONECT 2172 2171 2173 2175 CONECT 2173 2158 2172 2195 CONECT 2174 2171 CONECT 2175 2172 2176 CONECT 2176 2175 CONECT 2177 2158 2178 2196 CONECT 2178 2177 2179 2181 CONECT 2179 2178 2180 2182 CONECT 2180 2159 2179 2196 CONECT 2181 2178 CONECT 2182 2179 2183 CONECT 2183 2182 CONECT 2184 2159 2185 2197 CONECT 2185 2184 2186 2188 CONECT 2186 2185 2187 2189 CONECT 2187 2156 2186 2197 CONECT 2188 2185 CONECT 2189 2186 2190 CONECT 2190 2189 2191 CONECT 2191 2190 2192 2193 CONECT 2192 2191 CONECT 2193 2191 CONECT 2194 2160 2163 2198 CONECT 2195 2170 2173 2198 CONECT 2196 2177 2180 2198 CONECT 2197 2184 2187 2198 CONECT 2198 650 2194 2195 2196 CONECT 2198 2197 CONECT 2199 2200 CONECT 2200 2199 CONECT 2201 2205 2232 CONECT 2202 2208 2215 CONECT 2203 2218 2222 CONECT 2204 2225 2229 CONECT 2205 2201 2206 2239 CONECT 2206 2205 2207 2210 CONECT 2207 2206 2208 2209 CONECT 2208 2202 2207 2239 CONECT 2209 2207 CONECT 2210 2206 2211 CONECT 2211 2210 2212 CONECT 2212 2211 2213 2214 CONECT 2213 2212 CONECT 2214 2212 CONECT 2215 2202 2216 2240 CONECT 2216 2215 2217 2219 CONECT 2217 2216 2218 2220 CONECT 2218 2203 2217 2240 CONECT 2219 2216 CONECT 2220 2217 2221 CONECT 2221 2220 CONECT 2222 2203 2223 2241 CONECT 2223 2222 2224 2226 CONECT 2224 2223 2225 2227 CONECT 2225 2204 2224 2241 CONECT 2226 2223 CONECT 2227 2224 2228 CONECT 2228 2227 CONECT 2229 2204 2230 2242 CONECT 2230 2229 2231 2233 CONECT 2231 2230 2232 2234 CONECT 2232 2201 2231 2242 CONECT 2233 2230 CONECT 2234 2231 2235 CONECT 2235 2234 2236 CONECT 2236 2235 2237 2238 CONECT 2237 2236 CONECT 2238 2236 CONECT 2239 2205 2208 2243 CONECT 2240 2215 2218 2243 CONECT 2241 2222 2225 2243 CONECT 2242 2229 2232 2243 CONECT 2243 1764 2239 2240 2241 CONECT 2243 2242 CONECT 2244 2245 CONECT 2245 2244 MASTER 211 0 4 18 0 0 0 12 2243 2 94 23 END