HEADER IMMUNE SYSTEM 07-FEB-23 8I9M TITLE THE RAGE AND HMGB1 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIGH MOBILITY GROUP PROTEIN B1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HIGH MOBILITY GROUP PROTEIN 1,HMG-1; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: ADVANCED GLYCOSYLATION END PRODUCT-SPECIFIC RECEPTOR; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: RECEPTOR FOR ADVANCED GLYCOSYLATION END PRODUCTS; 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: HMGB1, HMG1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: AGER, RAGE; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RAGE, HMGB1, INFLAMMATION, IMMUNE SYSTEM EXPDTA ELECTRON MICROSCOPY AUTHOR C.W.HAN,H.J.KIM REVDAT 1 14-FEB-24 8I9M 0 JRNL AUTH C.W.HAN,H.J.KIM JRNL TITL THE RAGE AND HMGB1 COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 5.19 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) : 5.190 REMARK 3 NUMBER OF PARTICLES : 121467 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 8I9M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1300035226. 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 : THE RAGE AND HMGB1 COMPLEX 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 : TFS GLACIOS REMARK 245 DETECTOR TYPE : FEI FALCON III (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : DARK FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 3999.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL 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: DIMERIC 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS B 38 CB CYS B 38 SG -0.133 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 LEU B 34 CA - CB - CG ANGL. DEV. = 20.0 DEGREES REMARK 500 LEU B 49 CA - CB - CG ANGL. DEV. = 26.8 DEGREES REMARK 500 GLU B 94 CA - CB - CG ANGL. DEV. = 13.4 DEGREES REMARK 500 LYS B 123 C - N - CA ANGL. DEV. = 31.1 DEGREES REMARK 500 LEU B 133 CA - CB - CG ANGL. DEV. = 16.1 DEGREES REMARK 500 LEU B 159 CA - CB - CG ANGL. DEV. = -15.5 DEGREES REMARK 500 LEU B 185 CB - CG - CD2 ANGL. DEV. = -12.9 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 LYS A 96 -177.92 -69.58 REMARK 500 ASN A 134 33.31 -88.87 REMARK 500 ASP A 139 -62.50 -94.76 REMARK 500 ASP A 140 45.13 -143.75 REMARK 500 ALA A 148 112.41 -161.87 REMARK 500 ALA B 28 -153.95 -159.21 REMARK 500 ARG B 29 -167.08 -76.44 REMARK 500 LEU B 36 -165.51 -72.24 REMARK 500 LYS B 37 74.37 -60.78 REMARK 500 PRO B 46 -137.34 -87.90 REMARK 500 ARG B 48 5.55 -152.55 REMARK 500 LEU B 49 -144.94 -145.37 REMARK 500 TRP B 51 87.16 -151.71 REMARK 500 LYS B 52 -148.78 -75.24 REMARK 500 ASN B 54 34.13 88.82 REMARK 500 LYS B 62 -158.19 -156.97 REMARK 500 SER B 74 -70.19 -43.88 REMARK 500 GLN B 100 77.82 -100.10 REMARK 500 MET B 102 97.77 -50.70 REMARK 500 ASN B 103 -68.08 -102.77 REMARK 500 ARG B 104 -39.52 -142.24 REMARK 500 GLN B 119 -156.48 -149.01 REMARK 500 LYS B 123 155.53 -41.53 REMARK 500 ASP B 128 80.71 62.54 REMARK 500 SER B 131 -61.00 -109.75 REMARK 500 SER B 146 -173.03 -177.27 REMARK 500 SER B 149 -161.29 -173.86 REMARK 500 ALA B 152 -71.68 -56.01 REMARK 500 THR B 154 -160.42 -125.21 REMARK 500 LEU B 159 117.83 -33.78 REMARK 500 ASP B 160 77.60 54.18 REMARK 500 ASN B 167 68.05 61.35 REMARK 500 LYS B 169 -0.03 65.75 REMARK 500 LEU B 185 14.51 -143.17 REMARK 500 THR B 187 -152.86 -147.16 REMARK 500 MET B 193 56.66 -91.91 REMARK 500 PRO B 202 78.30 -64.36 REMARK 500 ARG B 203 52.53 -154.89 REMARK 500 THR B 205 145.19 -39.13 REMARK 500 PHE B 206 113.51 -165.61 REMARK 500 SER B 207 119.63 -167.17 REMARK 500 SER B 211 154.71 -47.60 REMARK 500 PRO B 215 46.20 -80.64 REMARK 500 THR B 222 -153.29 -144.96 REMARK 500 PRO B 224 -171.57 -69.22 REMARK 500 PRO B 232 47.01 -90.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PHE A 89 LYS A 90 -141.07 REMARK 500 ASP A 91 PRO A 92 -145.33 REMARK 500 ASN A 93 ALA A 94 -147.79 REMARK 500 ALA A 94 PRO A 95 -137.18 REMARK 500 ARG A 97 PRO A 98 -135.77 REMARK 500 ARG A 110 PRO A 111 -130.29 REMARK 500 GLU A 116 HIS A 117 -149.75 REMARK 500 GLY A 130 GLU A 131 -148.81 REMARK 500 GLN A 142 PRO A 143 -149.50 REMARK 500 LYS A 150 LEU A 151 -140.22 REMARK 500 LYS A 152 GLU A 153 -121.13 REMARK 500 ALA B 28 ARG B 29 -138.24 REMARK 500 ARG B 29 ILE B 30 -114.75 REMARK 500 ILE B 30 GLY B 31 146.44 REMARK 500 LEU B 34 VAL B 35 146.39 REMARK 500 LEU B 36 LYS B 37 -128.78 REMARK 500 PRO B 42 LYS B 43 -143.08 REMARK 500 PRO B 46 GLN B 47 -132.06 REMARK 500 TRP B 51 LYS B 52 -124.91 REMARK 500 LYS B 52 LEU B 53 -127.71 REMARK 500 ASN B 54 THR B 55 148.44 REMARK 500 ALA B 60 TRP B 61 -137.58 REMARK 500 SER B 65 PRO B 66 143.66 REMARK 500 ALA B 76 ARG B 77 147.53 REMARK 500 LEU B 84 PHE B 85 -143.44 REMARK 500 PRO B 87 ALA B 88 -146.29 REMARK 500 ARG B 98 CYS B 99 -149.67 REMARK 500 ALA B 101 MET B 102 -138.07 REMARK 500 MET B 102 ASN B 103 143.01 REMARK 500 ASN B 103 ARG B 104 137.93 REMARK 500 ARG B 104 ASN B 105 -142.96 REMARK 500 ASN B 105 GLY B 106 -30.25 REMARK 500 GLY B 106 LYS B 107 -149.18 REMARK 500 GLY B 142 THR B 143 -136.54 REMARK 500 CYS B 144 VAL B 145 -146.14 REMARK 500 VAL B 145 SER B 146 146.57 REMARK 500 HIS B 158 LEU B 159 -118.05 REMARK 500 LEU B 159 ASP B 160 145.95 REMARK 500 ASP B 160 GLY B 161 145.82 REMARK 500 GLU B 191 LEU B 192 -147.16 REMARK 500 ARG B 203 PRO B 204 146.35 REMARK 500 CYS B 208 SER B 209 -144.54 REMARK 500 THR B 222 ALA B 223 -149.52 REMARK 500 ILE B 225 GLN B 226 -141.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-35276 RELATED DB: EMDB REMARK 900 THE RAGE AND HMGB1 COMPLEX DBREF 8I9M A 89 163 UNP P09429 HMGB1_HUMAN 89 163 DBREF 8I9M B 23 233 UNP Q15109 RAGE_HUMAN 23 233 SEQRES 1 A 75 PHE LYS ASP PRO ASN ALA PRO LYS ARG PRO PRO SER ALA SEQRES 2 A 75 PHE PHE LEU PHE CYS SER GLU TYR ARG PRO LYS ILE LYS SEQRES 3 A 75 GLY GLU HIS PRO GLY LEU SER ILE GLY ASP VAL ALA LYS SEQRES 4 A 75 LYS LEU GLY GLU MET TRP ASN ASN THR ALA ALA ASP ASP SEQRES 5 A 75 LYS GLN PRO TYR GLU LYS LYS ALA ALA LYS LEU LYS GLU SEQRES 6 A 75 LYS TYR GLU LYS ASP ILE ALA ALA TYR ARG SEQRES 1 B 211 ALA GLN ASN ILE THR ALA ARG ILE GLY GLU PRO LEU VAL SEQRES 2 B 211 LEU LYS CYS LYS GLY ALA PRO LYS LYS PRO PRO GLN ARG SEQRES 3 B 211 LEU GLU TRP LYS LEU ASN THR GLY ARG THR GLU ALA TRP SEQRES 4 B 211 LYS VAL LEU SER PRO GLN GLY GLY GLY PRO TRP ASP SER SEQRES 5 B 211 VAL ALA ARG VAL LEU PRO ASN GLY SER LEU PHE LEU PRO SEQRES 6 B 211 ALA VAL GLY ILE GLN ASP GLU GLY ILE PHE ARG CYS GLN SEQRES 7 B 211 ALA MET ASN ARG ASN GLY LYS GLU THR LYS SER ASN TYR SEQRES 8 B 211 ARG VAL ARG VAL TYR GLN ILE PRO GLY LYS PRO GLU ILE SEQRES 9 B 211 VAL ASP SER ALA SER GLU LEU THR ALA GLY VAL PRO ASN SEQRES 10 B 211 LYS VAL GLY THR CYS VAL SER GLU GLY SER TYR PRO ALA SEQRES 11 B 211 GLY THR LEU SER TRP HIS LEU ASP GLY LYS PRO LEU VAL SEQRES 12 B 211 PRO ASN GLU LYS GLY VAL SER VAL LYS GLU GLN THR ARG SEQRES 13 B 211 ARG HIS PRO GLU THR GLY LEU PHE THR LEU GLN SER GLU SEQRES 14 B 211 LEU MET VAL THR PRO ALA ARG GLY GLY ASP PRO ARG PRO SEQRES 15 B 211 THR PHE SER CYS SER PHE SER PRO GLY LEU PRO ARG HIS SEQRES 16 B 211 ARG ALA LEU ARG THR ALA PRO ILE GLN PRO ARG VAL TRP SEQRES 17 B 211 GLU PRO VAL HELIX 1 AA1 SER A 121 ALA A 126 5 6 HELIX 2 AA2 GLU A 131 THR A 136 5 6 HELIX 3 AA3 GLY B 69 ASP B 73 5 5 SHEET 1 AA1 2 PHE B 97 ARG B 98 0 SHEET 2 AA1 2 GLU B 108 THR B 109 -1 O THR B 109 N PHE B 97 SSBOND 1 CYS B 38 CYS B 99 1555 1555 2.02 SSBOND 2 CYS B 144 CYS B 208 1555 1555 2.02 CISPEP 1 PRO B 45 PRO B 46 0 -13.40 CISPEP 2 TYR B 150 PRO B 151 0 -5.55 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