HEADER OXYGEN BINDING 25-SEP-23 8WIX TITLE CRYO-EM STRUCTURE OF ALLIGATOR HAEMOGLOBIN IN CARBONMONOXY 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: ALLIGATOR MISSISSIPPIENSIS; SOURCE 3 ORGANISM_COMMON: AMERICAN ALLIGATOR; SOURCE 4 ORGANISM_TAXID: 8496; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: ALLIGATOR MISSISSIPPIENSIS; SOURCE 7 ORGANISM_COMMON: AMERICAN ALLIGATOR; SOURCE 8 ORGANISM_TAXID: 8496 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 8WIX 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. 2.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EPU, CRYOSPARC, COOT, ISOLDE, UCSF REMARK 3 CHIMERAX, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC, SERVALCAT 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) : 2.290 REMARK 3 NUMBER OF PARTICLES : 751964 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 8WIX 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_1300041282. 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 : ALLIGATOR HAEMOGLOBIN IN REMARK 245 CARBONMONOXY 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 : 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) : 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 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 FE HEM B 201 C CMO B 202 1.96 REMARK 500 FE HEM A 201 C CMO A 202 1.99 REMARK 500 OD1 ASN B 80 O HOH B 301 1.99 REMARK 500 O LEU B 78 O HOH B 302 2.17 REMARK 500 ND1 HIS B 84 O HOH B 303 2.18 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 LYS B 47 104.11 -35.24 REMARK 500 MET B 48 49.20 -145.12 REMARK 500 HIS B 77 47.73 -147.31 REMARK 500 SER B 123 171.33 -55.77 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 82 0.08 SIDE CHAIN REMARK 500 ARG A 92 0.08 SIDE CHAIN REMARK 500 ARG B 8 0.09 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 89.3 REMARK 620 3 HEM A 201 NB 87.1 88.0 REMARK 620 4 HEM A 201 NC 96.4 171.2 85.6 REMARK 620 5 HEM A 201 ND 99.2 93.3 173.6 92.5 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 91.0 REMARK 620 3 HEM B 201 NB 92.0 87.8 REMARK 620 4 HEM B 201 NC 92.3 174.8 88.2 REMARK 620 5 HEM B 201 ND 92.1 92.4 176.0 91.4 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-37571 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF ALLIGATOR HAEMOGLOBIN IN CARBONMONOXY FORM DBREF 8WIX A 0 141 UNP P01999 HBA_ALLMI 1 142 DBREF 8WIX B 1 146 UNP P02130 HBB_ALLMI 1 146 SEQRES 1 A 142 MET VAL LEU SER MET GLU ASP LYS SER ASN VAL LYS ALA SEQRES 2 A 142 ILE TRP GLY LYS ALA SER GLY HIS LEU GLU GLU TYR GLY SEQRES 3 A 142 ALA GLU ALA LEU GLU ARG MET PHE CYS ALA TYR PRO GLN SEQRES 4 A 142 THR LYS ILE TYR PHE PRO HIS PHE ASP MET SER HIS ASN SEQRES 5 A 142 SER ALA GLN ILE ARG ALA HIS GLY LYS LYS VAL PHE SER SEQRES 6 A 142 ALA LEU HIS GLU ALA VAL ASN HIS ILE ASP ASP LEU PRO SEQRES 7 A 142 GLY ALA LEU CYS ARG LEU SER GLU LEU HIS ALA HIS SER SEQRES 8 A 142 LEU ARG VAL ASP PRO VAL ASN PHE LYS PHE LEU ALA HIS SEQRES 9 A 142 CYS VAL LEU VAL VAL PHE ALA ILE HIS HIS PRO SER ALA SEQRES 10 A 142 LEU SER PRO GLU ILE HIS ALA SER LEU ASP LYS PHE LEU SEQRES 11 A 142 CYS ALA VAL SER ALA VAL LEU THR SER LYS TYR ARG SEQRES 1 B 146 ALA SER PHE ASP ALA HIS GLU ARG LYS PHE ILE VAL ASP SEQRES 2 B 146 LEU TRP ALA LYS VAL ASP VAL ALA GLN CYS GLY ALA ASP SEQRES 3 B 146 ALA LEU SER ARG MET LEU ILE VAL TYR PRO TRP LYS ARG SEQRES 4 B 146 ARG TYR PHE GLU HIS PHE GLY LYS MET CYS ASN ALA HIS SEQRES 5 B 146 ASP ILE LEU HIS ASN SER LYS VAL GLN GLU HIS GLY LYS SEQRES 6 B 146 LYS VAL LEU ALA SER PHE GLY GLU ALA VAL LYS HIS LEU SEQRES 7 B 146 ASP ASN ILE LYS GLY HIS PHE ALA ASN LEU SER LYS LEU SEQRES 8 B 146 HIS CYS GLU LYS PHE HIS VAL ASP PRO GLU ASN PHE LYS SEQRES 9 B 146 LEU LEU GLY ASP ILE ILE ILE ILE VAL LEU ALA ALA HIS SEQRES 10 B 146 HIS PRO GLU ASP PHE SER VAL GLU CYS HIS ALA ALA PHE SEQRES 11 B 146 GLN LYS LEU VAL ARG GLN VAL ALA ALA ALA LEU ALA ALA SEQRES 12 B 146 GLU 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) FORMUL 7 HOH *117(H2 O) HELIX 1 AA1 SER A 3 SER A 18 1 16 HELIX 2 AA2 HIS A 20 TYR 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 HIS A 113 1 19 HELIX 8 AA8 SER A 118 THR A 137 1 20 HELIX 9 AA9 ASP B 4 ALA B 16 1 13 HELIX 10 AB1 ASP B 19 TYR B 35 1 17 HELIX 11 AB2 PRO B 36 GLY B 46 5 11 HELIX 12 AB3 ASN B 50 HIS B 56 1 7 HELIX 13 AB4 ASN B 57 GLY B 72 1 16 HELIX 14 AB5 GLU B 73 ASP B 79 5 7 HELIX 15 AB6 ASN B 80 LYS B 95 1 16 HELIX 16 AB7 PRO B 100 HIS B 118 1 19 HELIX 17 AB8 SER B 123 ALA B 142 1 20 LINK NE2 HIS A 87 FE HEM A 201 1555 1555 2.19 LINK NE2 HIS B 92 FE HEM B 201 1555 1555 2.35 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