HEADER IMMUNE SYSTEM 08-OCT-18 6MPP TITLE HLA-A*01:01 COMPLEX WITH NRAS Q61K PEPTIDE BY NMR COMPND MOL_ID: 1; COMPND 2 MOLECULE: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-1 ALPHA CHAIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 25-303; COMPND 5 SYNONYM: MHC CLASS I ANTIGEN A*1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: NRAS Q61K PEPTIDE; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: BETA-2-MICROGLOBULIN; COMPND 13 CHAIN: C; COMPND 14 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: HLA-A, HLAA; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 14 MOL_ID: 3; SOURCE 15 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 16 ORGANISM_COMMON: HUMAN; SOURCE 17 ORGANISM_TAXID: 9606; SOURCE 18 GENE: B2M, CDABP0092, HDCMA22P; SOURCE 19 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS IMMUNE SYSTEM EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR D.FLORES-SOLIS,A.C.MCSHAN,N.G.SGOURAKIS REVDAT 3 16-MAR-22 6MPP 1 TITLE COMPND REVDAT 2 18-DEC-19 6MPP 1 REMARK REVDAT 1 16-OCT-19 6MPP 0 JRNL AUTH D.FLORES-SOLIS,A.C.MCSHAN,N.G.SGOURAKIS JRNL TITL MHC-I COMPLEX DETERMINED BY NMR JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CS-ROSETTA REMARK 3 AUTHORS : SHEN, VERNON, BAKER AND BAX REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURE IS CALCULATED BASED ON NMR REMARK 3 CONSTRAINTS REMARK 4 REMARK 4 6MPP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1000237361. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : 20 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 300 UM [U-99% 13C; U-99% 15N] REMARK 210 MHC-I HLA-A01:01, 300 UM NRAS REMARK 210 Q16K, 300 UM HB2M, 90% H2O/10% REMARK 210 D2O; 180 UM [U-15N; U-2H]; [U- REMARK 210 15N; U-2H; METHYL-1H; METHYL-13C] REMARK 210 -ALA, ILE, LEU & VAL MHC-I HLA- REMARK 210 A01:01, 180 UM NRAS Q16K, 180 UM REMARK 210 HB2M, 90% H2O/10% D2O; 170 UM [U- REMARK 210 15N; U-2H]; [U-15N; U-2H; METHYL- REMARK 210 1H; METHYL-13C]-ALA, ILE, LEU & REMARK 210 VAL MHC-I HLA-A01:01, 170 UM REMARK 210 NRAS Q16K, 170 UM HB2M, 100% D2O; REMARK 210 210 UM [U-15N; U-2H]; [U-15N; U- REMARK 210 2H; METHYL-1H; METHYL-13C]-ALA, REMARK 210 ILE, LEU & VAL; [U-13C; U-15N]- REMARK 210 PHE & TYR MHC-I HLA-A01:01, 210 REMARK 210 UM [U-15N] NRAS Q16K, 210 UM [U- REMARK 210 2H] HB2M, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-1H FILTERED- REMARK 210 TOCSY; 3D HNCO; 3D HNCA; 3D REMARK 210 HNCACB; 3D HN(COCA)CB; 3D REMARK 210 CMETHYL-CMETHYLHMETHYL; 3D N- REMARK 210 CMETHYLHMETHYL; 3D N-NHAMIDE; 3D REMARK 210 HMETHYL-CMETHYLHMETHYL; 3D 1H- REMARK 210 13C FILTERED-NOESY; 3D CAROMATIC- REMARK 210 CMETHYLHMETHYL; 3D HMETHYL- REMARK 210 CAROHARO REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY NMRFAM, CS-ROSETTA REMARK 210 METHOD USED : DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 5000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 GLU A 275 REMARK 465 LEU A 276 REMARK 465 SER A 277 REMARK 465 SER A 278 REMARK 465 GLN A 279 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 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 1 ASP A 29 -110.46 49.87 REMARK 500 1 LEU A 110 -62.39 -106.82 REMARK 500 1 TYR A 123 -74.46 -108.09 REMARK 500 1 GLN A 226 -61.16 -109.41 REMARK 500 1 LYS B 7 42.74 -90.02 REMARK 500 1 PRO C 33 -157.01 -88.94 REMARK 500 1 SER C 58 -167.78 -103.80 REMARK 500 2 ASP A 29 -110.46 49.87 REMARK 500 2 LEU A 110 -62.39 -106.82 REMARK 500 2 TYR A 123 -74.46 -108.09 REMARK 500 2 GLN A 226 -61.16 -109.41 REMARK 500 2 LYS B 7 74.17 -67.90 REMARK 500 2 PRO C 33 -157.01 -88.94 REMARK 500 2 SER C 58 -167.78 -103.80 REMARK 500 3 ASP A 29 -110.46 49.87 REMARK 500 3 LEU A 110 -62.39 -106.82 REMARK 500 3 TYR A 123 -74.46 -108.09 REMARK 500 3 GLN A 226 -61.16 -109.41 REMARK 500 3 PRO C 33 -157.01 -88.94 REMARK 500 3 SER C 58 -167.78 -103.80 REMARK 500 4 ASP A 29 -110.46 49.87 REMARK 500 4 LEU A 110 -62.39 -106.82 REMARK 500 4 TYR A 123 -74.46 -108.09 REMARK 500 4 GLN A 226 -61.16 -109.41 REMARK 500 4 GLU B 8 44.16 -140.17 REMARK 500 4 PRO C 33 -157.01 -88.94 REMARK 500 4 SER C 58 -167.78 -103.80 REMARK 500 5 ASP A 29 -110.46 49.87 REMARK 500 5 LEU A 110 -62.39 -106.82 REMARK 500 5 TYR A 123 -74.46 -108.09 REMARK 500 5 GLN A 226 -61.16 -109.41 REMARK 500 5 PRO C 33 -157.01 -88.94 REMARK 500 5 SER C 58 -167.78 -103.80 REMARK 500 6 ASP A 29 -110.46 49.87 REMARK 500 6 LEU A 110 -62.39 -106.82 REMARK 500 6 TYR A 123 -74.46 -108.09 REMARK 500 6 GLN A 226 -61.16 -109.41 REMARK 500 6 ALA B 5 88.52 -68.63 REMARK 500 6 PRO C 33 -157.01 -88.94 REMARK 500 6 SER C 58 -167.78 -103.80 REMARK 500 7 ASP A 29 -110.46 49.87 REMARK 500 7 LEU A 110 -62.39 -106.82 REMARK 500 7 TYR A 123 -74.46 -108.09 REMARK 500 7 GLN A 226 -61.16 -109.41 REMARK 500 7 LYS B 7 74.32 -67.93 REMARK 500 7 PRO C 33 -157.01 -88.94 REMARK 500 7 SER C 58 -167.78 -103.80 REMARK 500 8 ASP A 29 -110.46 49.87 REMARK 500 8 LEU A 110 -62.39 -106.82 REMARK 500 8 TYR A 123 -74.46 -108.09 REMARK 500 REMARK 500 THIS ENTRY HAS 68 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 27632 RELATED DB: BMRB DBREF 6MPP A 1 279 UNP P30443 1A01_HUMAN 25 303 DBREF 6MPP B 1 10 PDB 6MPP 6MPP 1 10 DBREF 6MPP C 2 100 UNP P61769 B2MG_HUMAN 21 119 SEQADV 6MPP MET C 1 UNP P61769 INITIATING METHIONINE SEQRES 1 A 279 GLY SER HIS SER MET ARG TYR PHE PHE THR SER VAL SER SEQRES 2 A 279 ARG PRO GLY ARG GLY GLU PRO ARG PHE ILE ALA VAL GLY SEQRES 3 A 279 TYR VAL ASP ASP THR GLN PHE VAL ARG PHE ASP SER ASP SEQRES 4 A 279 ALA ALA SER GLN LYS MET GLU PRO ARG ALA PRO TRP ILE SEQRES 5 A 279 GLU GLN GLU GLY PRO GLU TYR TRP ASP GLN GLU THR ARG SEQRES 6 A 279 ASN MET LYS ALA HIS SER GLN THR ASP ARG ALA ASN LEU SEQRES 7 A 279 GLY THR LEU ARG GLY TYR TYR ASN GLN SER GLU ASP GLY SEQRES 8 A 279 SER HIS THR ILE GLN ILE MET TYR GLY CYS ASP VAL GLY SEQRES 9 A 279 PRO ASP GLY ARG PHE LEU ARG GLY TYR ARG GLN ASP ALA SEQRES 10 A 279 TYR ASP GLY LYS ASP TYR ILE ALA LEU ASN GLU ASP LEU SEQRES 11 A 279 ARG SER TRP THR ALA ALA ASP MET ALA ALA GLN ILE THR SEQRES 12 A 279 LYS ARG LYS TRP GLU ALA VAL HIS ALA ALA GLU GLN ARG SEQRES 13 A 279 ARG VAL TYR LEU GLU GLY ARG CYS VAL ASP GLY LEU ARG SEQRES 14 A 279 ARG TYR LEU GLU ASN GLY LYS GLU THR LEU GLN ARG THR SEQRES 15 A 279 ASP PRO PRO LYS THR HIS MET THR HIS HIS PRO ILE SER SEQRES 16 A 279 ASP HIS GLU ALA THR LEU ARG CYS TRP ALA LEU GLY PHE SEQRES 17 A 279 TYR PRO ALA GLU ILE THR LEU THR TRP GLN ARG ASP GLY SEQRES 18 A 279 GLU ASP GLN THR GLN ASP THR GLU LEU VAL GLU THR ARG SEQRES 19 A 279 PRO ALA GLY ASP GLY THR PHE GLN LYS TRP ALA ALA VAL SEQRES 20 A 279 VAL VAL PRO SER GLY GLU GLU GLN ARG TYR THR CYS HIS SEQRES 21 A 279 VAL GLN HIS GLU GLY LEU PRO LYS PRO LEU THR LEU ARG SEQRES 22 A 279 TRP GLU LEU SER SER GLN SEQRES 1 B 10 ILE LEU ASP THR ALA GLY LYS GLU GLU TYR SEQRES 1 C 100 MET ILE GLN ARG THR PRO LYS ILE GLN VAL TYR SER ARG SEQRES 2 C 100 HIS PRO ALA GLU ASN GLY LYS SER ASN PHE LEU ASN CYS SEQRES 3 C 100 TYR VAL SER GLY PHE HIS PRO SER ASP ILE GLU VAL ASP SEQRES 4 C 100 LEU LEU LYS ASN GLY GLU ARG ILE GLU LYS VAL GLU HIS SEQRES 5 C 100 SER ASP LEU SER PHE SER LYS ASP TRP SER PHE TYR LEU SEQRES 6 C 100 LEU TYR TYR THR GLU PHE THR PRO THR GLU LYS ASP GLU SEQRES 7 C 100 TYR ALA CYS ARG VAL ASN HIS VAL THR LEU SER GLN PRO SEQRES 8 C 100 LYS ILE VAL LYS TRP ASP ARG ASP MET HELIX 1 AA1 ALA A 49 GLU A 53 5 5 HELIX 2 AA2 GLY A 56 TYR A 85 1 30 HELIX 3 AA3 ASP A 137 VAL A 150 1 14 HELIX 4 AA4 HIS A 151 GLY A 162 1 12 HELIX 5 AA5 GLY A 162 GLY A 175 1 14 HELIX 6 AA6 GLY A 175 GLN A 180 1 6 HELIX 7 AA7 GLU A 253 GLN A 255 5 3 SHEET 1 AA1 8 GLU A 46 PRO A 47 0 SHEET 2 AA1 8 THR A 31 ASP A 37 -1 N ARG A 35 O GLU A 46 SHEET 3 AA1 8 ARG A 21 VAL A 28 -1 N VAL A 28 O THR A 31 SHEET 4 AA1 8 HIS A 3 VAL A 12 -1 N ARG A 6 O TYR A 27 SHEET 5 AA1 8 THR A 94 VAL A 103 -1 O ILE A 97 N PHE A 9 SHEET 6 AA1 8 PHE A 109 TYR A 118 -1 O LEU A 110 N ASP A 102 SHEET 7 AA1 8 LYS A 121 LEU A 126 -1 O LYS A 121 N TYR A 118 SHEET 8 AA1 8 TRP A 133 ALA A 135 -1 O THR A 134 N ALA A 125 SHEET 1 AA2 4 HIS A 188 PRO A 193 0 SHEET 2 AA2 4 ALA A 199 TRP A 204 -1 O TRP A 204 N HIS A 188 SHEET 3 AA2 4 TRP A 244 VAL A 248 -1 O ALA A 245 N CYS A 203 SHEET 4 AA2 4 THR A 228 LEU A 230 -1 N GLU A 229 O ALA A 246 SHEET 1 AA3 4 GLU A 222 GLN A 224 0 SHEET 2 AA3 4 THR A 214 ARG A 219 -1 N ARG A 219 O GLU A 222 SHEET 3 AA3 4 TYR A 257 GLN A 262 -1 O HIS A 260 N THR A 216 SHEET 4 AA3 4 LEU A 270 LEU A 272 -1 O LEU A 272 N CYS A 259 SHEET 1 AA4 2 ARG A 234 PRO A 235 0 SHEET 2 AA4 2 PHE A 241 GLN A 242 -1 O GLN A 242 N ARG A 234 SHEET 1 AA5 4 LYS C 7 SER C 12 0 SHEET 2 AA5 4 ASN C 22 PHE C 31 -1 O ASN C 25 N TYR C 11 SHEET 3 AA5 4 PHE C 63 PHE C 71 -1 O THR C 69 N LEU C 24 SHEET 4 AA5 4 GLU C 51 HIS C 52 -1 N GLU C 51 O TYR C 68 SHEET 1 AA6 4 LYS C 7 SER C 12 0 SHEET 2 AA6 4 ASN C 22 PHE C 31 -1 O ASN C 25 N TYR C 11 SHEET 3 AA6 4 PHE C 63 PHE C 71 -1 O THR C 69 N LEU C 24 SHEET 4 AA6 4 SER C 56 PHE C 57 -1 N SER C 56 O TYR C 64 SHEET 1 AA7 4 GLU C 45 ARG C 46 0 SHEET 2 AA7 4 ILE C 36 LYS C 42 -1 N LYS C 42 O GLU C 45 SHEET 3 AA7 4 TYR C 79 HIS C 85 -1 O ALA C 80 N LEU C 41 SHEET 4 AA7 4 LYS C 92 LYS C 95 -1 O LYS C 92 N VAL C 83 SSBOND 1 CYS A 101 CYS A 164 1555 1555 2.09 SSBOND 2 CYS A 203 CYS A 259 1555 1555 2.05 SSBOND 3 CYS C 26 CYS C 81 1555 1555 2.05 CISPEP 1 TYR A 209 PRO A 210 1 16.47 CISPEP 2 HIS C 32 PRO C 33 1 12.38 CISPEP 3 TYR A 209 PRO A 210 2 16.47 CISPEP 4 HIS C 32 PRO C 33 2 12.38 CISPEP 5 TYR A 209 PRO A 210 3 16.47 CISPEP 6 HIS C 32 PRO C 33 3 12.38 CISPEP 7 TYR A 209 PRO A 210 4 16.47 CISPEP 8 HIS C 32 PRO C 33 4 12.38 CISPEP 9 TYR A 209 PRO A 210 5 16.47 CISPEP 10 HIS C 32 PRO C 33 5 12.38 CISPEP 11 TYR A 209 PRO A 210 6 16.47 CISPEP 12 HIS C 32 PRO C 33 6 12.38 CISPEP 13 TYR A 209 PRO A 210 7 16.47 CISPEP 14 HIS C 32 PRO C 33 7 12.38 CISPEP 15 TYR A 209 PRO A 210 8 16.47 CISPEP 16 HIS C 32 PRO C 33 8 12.38 CISPEP 17 TYR A 209 PRO A 210 9 16.47 CISPEP 18 HIS C 32 PRO C 33 9 12.38 CISPEP 19 TYR A 209 PRO A 210 10 16.47 CISPEP 20 HIS C 32 PRO C 33 10 12.38 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 MODEL 1