PDB Short entry for 2RVB HEADER DNA BINDING PROTEIN/TRANSCRIPTION 01-JUL-15 2RVB TITLE SOLUTION STRUCTURE OF THE COMPLEX BETWEEN XPC ACIDIC DOMAIN AND TFIIH TITLE 2 P62 PH DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA REPAIR PROTEIN COMPLEMENTING XP-C CELLS; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: XERODERMA PIGMENTOSUM GROUP C-COMPLEMENTING PROTEIN, P125; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: GENERAL TRANSCRIPTION FACTOR IIH SUBUNIT 1; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: BASIC TRANSCRIPTION FACTOR 2 62 KDA SUBUNIT, BTF2 P62, COMPND 10 GENERAL TRANSCRIPTION FACTOR IIH POLYPEPTIDE 1, TFIIH BASAL COMPND 11 TRANSCRIPTION FACTOR COMPLEX P62 SUBUNIT; COMPND 12 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: XPC, XPCC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET15B; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: GTF2H1, BTF2; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_VECTOR: PGEX-4T KEYWDS DNA REPAIR, HUMAN XPC, ACIDIC DOMAIN, GENERAL TRANSCRIPTION FACTOR, KEYWDS 2 HUMAN TFIIH P62, PH DOMAIN, DNA BINDING PROTEIN-TRANSCRIPTION KEYWDS 3 COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.OKUDA,Y.NISHIMURA REVDAT 2 07-JUN-17 2RVB 1 JRNL REVDAT 1 09-SEP-15 2RVB 0 JRNL AUTH M.OKUDA,M.KINOSHITA,E.KAKUMU,K.SUGASAWA,Y.NISHIMURA JRNL TITL STRUCTURAL INSIGHT INTO THE MECHANISM OF TFIIH RECOGNITION JRNL TITL 2 BY THE ACIDIC STRING OF THE NUCLEOTIDE EXCISION REPAIR JRNL TITL 3 FACTOR XPC. JRNL REF STRUCTURE V. 23 1827 2015 JRNL REFN ISSN 1878-4186 JRNL PMID 26278177 JRNL DOI 10.1016/J.STR.2015.07.009 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRDRAW, X-PLOR_NIH REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRDRAW), SCHWIETERS, KUSZEWSKI, TJANDRA AND REMARK 3 CLORE (X-PLOR_NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2RVB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000150310. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 305 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 0.02 REMARK 210 PRESSURE : AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 0.4 MM [U-99% 13C; U-99% 15N] REMARK 210 XPC ACIDIC DOMAIN-1, 0.48 MM REMARK 210 TFIIH P62 PH DOMAIN-2, 20 MM REMARK 210 POTASSIUM PHOSPHATE-3, 5 MM [U- REMARK 210 2H] DTT-4, 90% H2O/10% D2O; 0.4 REMARK 210 MM [U-99% 13C; U-99% 15N] XPC REMARK 210 ACIDIC DOMAIN-5, 0.48 MM TFIIH REMARK 210 P62 PH DOMAIN-6, 20 MM POTASSIUM REMARK 210 PHOSPHATE-7, 5 MM [U-2H] DTT-8, REMARK 210 100% D2O; 0.4 MM [U-99% 13C; U- REMARK 210 99% 15N] TFIIH P62 PH DOMAIN-9, REMARK 210 0.48 MM XPC ACIDIC DOMAIN-10, 20 REMARK 210 MM POTASSIUM PHOSPHATE-11, 5 MM REMARK 210 [U-2H] DTT-12, 90% H2O/10% D2O; REMARK 210 0.4 MM [U-99% 13C; U-99% 15N] REMARK 210 TFIIH P62 PH DOMAIN-13, 0.48 MM REMARK 210 XPC ACIDIC DOMAIN-14, 20 MM REMARK 210 POTASSIUM PHOSPHATE-15, 5 MM [U- REMARK 210 2H] DTT-16, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D HNCO; 3D REMARK 210 HBHA(CO)NH; 3D HCCH-TOCSY; 2D 1H- REMARK 210 13C HSQC AROMATIC; 3D HNHB; 3D REMARK 210 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 700 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW, X-PLOR_NIH, MOLMOL, REMARK 210 PROCHECKNMR REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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: 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 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 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A 105 REMARK 465 SER A 106 REMARK 465 HIS A 107 REMARK 465 MET A 108 REMARK 465 GLY B -1 REMARK 465 SER B 0 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 OE1 GLU A 135 HZ1 LYS B 54 1.52 REMARK 500 OE1 GLU A 138 HZ3 LYS B 104 1.55 REMARK 500 HZ3 LYS A 113 OE2 GLU A 130 1.55 REMARK 500 HZ1 LYS B 106 O ASN B 108 1.56 REMARK 500 HZ1 LYS B 93 OD1 ASP B 94 1.57 REMARK 500 OE1 GLU A 126 HZ2 LYS B 19 1.58 REMARK 500 OE1 GLU A 125 HZ1 LYS B 18 1.58 REMARK 500 OE1 GLU A 137 HZ3 LYS B 51 1.58 REMARK 500 OD1 ASP A 132 HZ1 LYS B 60 1.58 REMARK 500 OE1 GLU B 6 HH21 ARG B 30 1.59 REMARK 500 OE1 GLU A 130 HZ3 LYS B 18 1.59 REMARK 500 HZ1 LYS A 113 OE2 GLU A 125 1.59 REMARK 500 H GLU A 134 O ILE B 55 1.59 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 LYS A 113 -57.19 -173.65 REMARK 500 1 MET A 118 -39.85 -136.27 REMARK 500 1 ASN A 119 37.40 -150.07 REMARK 500 1 GLU A 124 -89.01 -105.17 REMARK 500 1 GLU A 126 -47.75 -135.95 REMARK 500 1 GLU A 128 141.56 -175.14 REMARK 500 1 ASP A 132 77.26 -162.04 REMARK 500 1 SER A 154 -61.33 70.62 REMARK 500 1 LYS B 14 70.44 15.94 REMARK 500 1 LYS B 19 3.72 83.58 REMARK 500 2 ARG A 114 -25.69 -144.33 REMARK 500 2 MET A 118 -76.76 -132.59 REMARK 500 2 ASN A 119 -55.38 178.62 REMARK 500 2 GLU A 124 178.91 67.01 REMARK 500 2 GLU A 125 88.91 48.09 REMARK 500 2 SER A 129 140.46 66.57 REMARK 500 2 GLU A 130 -59.55 -142.02 REMARK 500 2 ASP A 132 67.59 -152.10 REMARK 500 2 PRO A 142 99.65 -68.88 REMARK 500 2 SER A 150 28.40 -166.18 REMARK 500 2 SER A 154 -69.86 67.67 REMARK 500 2 ALA B 2 -59.18 72.10 REMARK 500 2 THR B 3 82.28 -151.20 REMARK 500 2 SER B 5 -166.64 -161.66 REMARK 500 2 VAL B 8 96.84 -69.94 REMARK 500 2 LYS B 14 73.33 15.97 REMARK 500 2 LYS B 19 7.20 80.09 REMARK 500 3 HIS A 111 106.52 64.73 REMARK 500 3 THR A 117 87.28 -157.36 REMARK 500 3 MET A 118 -56.48 -135.20 REMARK 500 3 ASN A 119 -62.53 172.11 REMARK 500 3 GLU A 126 -63.39 -169.21 REMARK 500 3 GLU A 127 85.05 -179.51 REMARK 500 3 GLU A 128 46.89 -99.73 REMARK 500 3 VAL A 147 31.83 -163.26 REMARK 500 3 ARG A 148 -21.11 -155.78 REMARK 500 3 GLU A 149 -67.98 -135.50 REMARK 500 3 SER A 154 -65.16 68.69 REMARK 500 3 LYS B 14 72.72 16.25 REMARK 500 3 GLU B 82 2.24 -64.35 REMARK 500 3 LYS B 104 109.96 -58.89 REMARK 500 4 LYS A 113 44.70 -84.36 REMARK 500 4 ALA A 116 -159.96 -124.05 REMARK 500 4 GLU A 120 -127.40 -78.55 REMARK 500 4 GLU A 138 108.57 -52.11 REMARK 500 4 VAL A 147 14.15 -149.89 REMARK 500 4 ALA A 152 73.87 -112.80 REMARK 500 4 ALA B 2 -146.63 -80.76 REMARK 500 4 SER B 4 -107.28 -116.20 REMARK 500 4 SER B 5 29.79 -167.07 REMARK 500 REMARK 500 THIS ENTRY HAS 315 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 11594 RELATED DB: BMRB DBREF 2RVB A 109 156 UNP Q01831 XPC_HUMAN 109 156 DBREF 2RVB B 1 108 UNP P32780 TF2H1_HUMAN 1 108 SEQADV 2RVB GLY A 105 UNP Q01831 EXPRESSION TAG SEQADV 2RVB SER A 106 UNP Q01831 EXPRESSION TAG SEQADV 2RVB HIS A 107 UNP Q01831 EXPRESSION TAG SEQADV 2RVB MET A 108 UNP Q01831 EXPRESSION TAG SEQADV 2RVB GLY B -1 UNP P32780 EXPRESSION TAG SEQADV 2RVB SER B 0 UNP P32780 EXPRESSION TAG SEQRES 1 A 52 GLY SER HIS MET ALA HIS HIS LEU LYS ARG GLY ALA THR SEQRES 2 A 52 MET ASN GLU ASP SER ASN GLU GLU GLU GLU GLU SER GLU SEQRES 3 A 52 ASN ASP TRP GLU GLU VAL GLU GLU LEU SER GLU PRO VAL SEQRES 4 A 52 LEU GLY ASP VAL ARG GLU SER THR ALA PHE SER ARG SER SEQRES 1 B 110 GLY SER MET ALA THR SER SER GLU GLU VAL LEU LEU ILE SEQRES 2 B 110 VAL LYS LYS VAL ARG GLN LYS LYS GLN ASP GLY ALA LEU SEQRES 3 B 110 TYR LEU MET ALA GLU ARG ILE ALA TRP ALA PRO GLU GLY SEQRES 4 B 110 LYS ASP ARG PHE THR ILE SER HIS MET TYR ALA ASP ILE SEQRES 5 B 110 LYS CYS GLN LYS ILE SER PRO GLU GLY LYS ALA LYS ILE SEQRES 6 B 110 GLN LEU GLN LEU VAL LEU HIS ALA GLY ASP THR THR ASN SEQRES 7 B 110 PHE HIS PHE SER ASN GLU SER THR ALA VAL LYS GLU ARG SEQRES 8 B 110 ASP ALA VAL LYS ASP LEU LEU GLN GLN LEU LEU PRO LYS SEQRES 9 B 110 PHE LYS ARG LYS ALA ASN HELIX 1 1 TYR B 47 ASP B 49 5 3 HELIX 2 2 THR B 84 LYS B 104 1 21 SHEET 1 A 8 THR B 42 MET B 46 0 SHEET 2 A 8 ARG B 30 ALA B 34 -1 N ILE B 31 O HIS B 45 SHEET 3 A 8 ASP B 21 MET B 27 -1 N ALA B 23 O ALA B 34 SHEET 4 A 8 LEU B 9 ARG B 16 -1 N VAL B 12 O LEU B 24 SHEET 5 A 8 ASP B 73 PHE B 79 -1 O HIS B 78 N ARG B 16 SHEET 6 A 8 ILE B 63 LEU B 69 -1 N LEU B 65 O PHE B 77 SHEET 7 A 8 ILE B 50 SER B 56 -1 N CYS B 52 O VAL B 68 SHEET 8 A 8 GLU A 134 GLU A 137 -1 N GLU A 134 O ILE B 55 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