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(-) Description

Title :  CRYSTAL STRUCTURE OF RAD4-RAD23 CROSSLINKED TO AN UNDAMAGED DNA
 
Authors :  J. -H. Min, X. Chen, Y. Kim
Date :  02 Mar 15  (Deposition) - 11 Mar 15  (Release) - 11 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.05
Chains :  Asym./Biol. Unit :  A,W,X,Y
Keywords :  Dna Damage Repair, Nucleotide Excision Repair, Protein-Dna Interactions, Protein-Dna Crosslinking, Protein-Dna Complex, Xeroderma Pigmentosum, Beta-Hairpin, Transglutaminase Domain, Disulfide Crosslinking, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Chen, Y. Velmurugu, G. Zheng, B. Park, Y. Shim, Y. Kim, L. Liu, B. Van Houten, C. He, A. Ansari, J. H. Min
Kinetic Gating Mechanism Of Dna Damage Recognition By Rad4/Xpc.
Nat Commun V. 6 5849 2015
PubMed-ID: 25562780  |  Reference-DOI: 10.1038/NCOMMS6849

(-) Compounds

Molecule 1 - DNA REPAIR PROTEIN RAD4
    Chains: A
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: HIGH FIVE CELLS (BTI-TN-5B1-4)
    Expression System Taxid: 7111
    Gene: RAD4, YER162C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / S288C)
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
 
Molecule 2 - UV EXCISION REPAIR PROTEIN RAD23
    Chains: X
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: HIGH FIVE CELLS (BTI-TN-5B1-4)
    Expression System Taxid: 7111
    Gene: RAD23, YEL037C, SYGP-ORF29
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / S288C)
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
 
Molecule 3 - DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*(G47) P*AP*CP*AP*TP*CP*CP*CP*CP*CP*GP*CP*TP*AP*CP*AP*A)-3')
    Chains: W
    Engineered: YES
    Expression System: SYNTHETIC CONSTRUCT
    Expression System Taxid: 32630
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
 
Molecule 4 - DNA (5'- D(*AP*TP*TP*GP*TP*AP*GP*CP*G*GP*GP*GP*AP*TP*GP*TP*CP*GP*AP*GP*TP*CP*A )-3')
    Chains: Y
    Engineered: YES
    Expression System: SYNTHETIC CONSTRUCT
    Expression System Taxid: 32630
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : AWXY

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1G471Mod. NucleotideN2-ETHANETHIOL-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 4YIR)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:131 -W:8

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4YIR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YIR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YIR)

(-) Exons   (0, 0)

(no "Exon" information available for 4YIR)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:499
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.ee...........hhhhhhhhh........hhhhhhhhhhhhheehhhhhhhhhhhhhhhh...eeeeeee.................hhhhhhh....eeeeeee....eeeeee.....eee.............hhhhhh...eeeee.....eeehhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.....hhhhhh....eee.hhh...eee.......eeee.......eeeeee...eee.eehhhhhh..eee.......eeeee...eeeeeehhh.eee...................ee..hhhhh...eeeee..hhhhhhhhhh....eee...ee.....ee..eeeeeee..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yir A 126 RTSRNCSSNEERKRRKYFHMLYLVCLMVHGFIRNEWINSKRLSRKLSNLVPEKVFELLHPQKDEELPLRSTRKLLDGLKKCMELWQKHWKITKKYDNEGLYMRTWKEIEMSANNKRKFKTLKRSDFLRAVSKGHGDPDISVQGFVAMLRACNVNARLIMSCQPPDFTNMKIDTSLNGNNAYKDMVKYPIFWCEVWDKFSKKWITVDPVNLKTIEQVRLHSKLAPKGVACCERNMLRYVIAYDRKYGCRDVTRRYAQWMNSKVRKRRITKDDFGEKWFRKVITALHHRKRTKIDDYEDQYFFRRDESEGIPDSVQDLKNHPYYVLEQDIKQTQIVKPGCKECGYLKVHGKVGKVLKVYAKRDIADLKSARQWYMNGRILKTGSRCKKVIKRTEEEDERLYSFEDTELYIPPLASASGEITKNTFGNIEVFAPTMIPGNCCLVENPVAIKAARFLGVEFAPAVTSFKFERGSTVKPVLSGIVVAKWLREAIETAIDGIEFI 632
                                   135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515||     533       543       553       563       573       583       593       603       613       623         
                                                                                                                                                                                                                                                                                                                                                                                                                                516|                                                                                                           
                                                                                                                                                                                                                                                                                                                                                                                                                                 525                                                                                                           


Chain W from PDB  Type:DNA  Length:24
                                                        
                 4yir W   1 TTGACTCxACATCCCCCGCTACAA  24
                                   |10        20    
                                   8-G47            


Chain X from PDB  Type:PROTEIN  Length:53
                                                                                     
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                 4yir X 256 GLTVEDLLSLRQVVSGNPEALAPLLENISARYPQLREHIMANPEVFVSMLLEA 308
                                   265       275       285       295       305   


Chain Y from PDB  Type:DNA  Length:23
                                                       
                 4yir Y   1 ATTGTAGCGGGGATGTCGAGTCA  24
                                    11        21   
                                    9|             
                                    11
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4YIR)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YIR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YIR)

(-) Gene Ontology  (24, 34)

Asymmetric/Biological Unit(hide GO term definitions)

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  RAD4_YEAST | P14736
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RAD23_YEAST | P32628: 1x3w 1x3z 2nbu 2nbw 2qsf 2qsg 2qsh 3esw 3m62
        RAD4_YEAST | P14736: 2m14 2qsf 2qsg 2qsh

(-) Related Entries Specified in the PDB File

4u29