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(-) Description

Title :  HUMAN P53 CORE DOMAIN WITH HOT SPOT MUTATION R273C AND SECOND-SITE SUPPRESSOR MUTATION T284R IN SEQUENCE-SPECIFIC COMPLEX WITH DNA
 
Authors :  A. Eldar, H. Rozenberg, Y. Diskin-Posner, Z. Shakked
Date :  09 Dec 12  (Deposition) - 14 Aug 13  (Release) - 23 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Metal-Binding, Loop-Sheet-Helix Motif, Transcription, Activator, Anti-Oncogene, Apoptosis, Cell Cycle, Disease Mutation, Rescue Mutation, Tumor Suppressor, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Eldar, H. Rozenberg, Y. Diskin-Posner, R. Rohs, Z. Shakked
Structural Studies Of P53 Inactivation By Dna-Contact Mutations And Its Rescue By Suppressor Mutations Via Alternative Protein-Dna Interactions.
Nucleic Acids Res. V. 41 8748 2013
PubMed-ID: 23863845  |  Reference-DOI: 10.1093/NAR/GKT630

(-) Compounds

Molecule 1 - CELLULAR TUMOR ANTIGEN P53
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-27-B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: DNA BINDING DOMAIN
    Gene: P53, TP53
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ANTIGEN NY-CO-13, PHOSPHOPROTEIN P53, TUMOR SUPPRESSOR P53
 
Molecule 2 - DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3')
    Chains: E, F, G, H
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit : ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 22)

Asymmetric/Biological Unit (3, 22)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2EDO16Ligand/Ion1,2-ETHANEDIOL
3ZN4Ligand/IonZINC ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:176 , HIS A:179 , CYS A:238 , CYS A:242BINDING SITE FOR RESIDUE ZN A 301
02AC2SOFTWARELYS A:120 , ARG A:280 , HOH A:434 , HOH A:462BINDING SITE FOR RESIDUE EDO A 302
03AC3SOFTWARELYS A:132 , SER A:240 , ARG A:248 , ARG A:249 , PRO A:250 , ILE A:251 , GLU A:271 , VAL A:272 , CYS A:273 , HOH A:454 , HOH A:543BINDING SITE FOR RESIDUE EDO A 303
04AC4SOFTWARELEU A:130 , ASN A:131 , GLU A:271 , SER B:95 , SER B:96BINDING SITE FOR RESIDUE EDO A 304
05AC5SOFTWAREALA A:138 , ASP A:184BINDING SITE FOR RESIDUE EDO A 305
06AC6SOFTWARELEU A:206 , ASP A:208 , ARG A:209 , HOH A:654 , SER C:116 , DG F:12 , HOH F:113BINDING SITE FOR RESIDUE EDO A 306
07AC7SOFTWARECYS B:176 , HIS B:179 , CYS B:238 , CYS B:242BINDING SITE FOR RESIDUE ZN B 301
08AC8SOFTWARELEU B:114 , PRO B:142 , HIS B:233 , HOH B:459 , HOH B:543BINDING SITE FOR RESIDUE EDO B 302
09AC9SOFTWAREALA B:138 , HOH B:454 , HOH B:497 , HOH B:577BINDING SITE FOR RESIDUE EDO B 303
10BC1SOFTWARESER B:185 , ACT B:305 , HOH B:561 , GLY D:199 , ASN D:200 , GLU D:221 , HOH D:445 , HOH D:519BINDING SITE FOR RESIDUE EDO B 304
11BC2SOFTWARESER B:183 , ASP B:184 , SER B:185 , EDO B:304 , HOH B:547 , HOH B:561 , HOH D:507BINDING SITE FOR RESIDUE ACT B 305
12BC3SOFTWARECYS C:176 , HIS C:179 , CYS C:238 , CYS C:242BINDING SITE FOR RESIDUE ZN C 301
13BC4SOFTWARELEU C:114 , PRO C:142 , HIS C:233 , HOH C:424 , HOH C:617BINDING SITE FOR RESIDUE EDO C 302
14BC5SOFTWARELEU C:130 , LYS C:132 , LYS C:164 , GLU C:271 , GLU C:285 , HOH C:528 , HOH C:639BINDING SITE FOR RESIDUE EDO C 303
15BC6SOFTWARELEU C:130 , ASN C:131 , GLU C:271 , HOH C:528 , HOH C:650 , SER D:96BINDING SITE FOR RESIDUE EDO C 304
16BC7SOFTWARECYS D:176 , HIS D:179 , CYS D:238 , CYS D:242BINDING SITE FOR RESIDUE ZN D 301
17BC8SOFTWARELYS B:139 , HOH B:413 , ALA D:138 , LYS D:139 , THR D:140 , GLU D:198BINDING SITE FOR RESIDUE EDO D 302
18BC9SOFTWAREPRO D:219 , HOH D:422 , HOH D:451 , HOH D:551BINDING SITE FOR RESIDUE EDO D 303
19CC1SOFTWAREPRO D:190 , TYR D:205 , ASP D:207 , HOH D:411BINDING SITE FOR RESIDUE EDO D 304
20CC2SOFTWARELEU D:114 , PRO D:142 , THR D:231 , HIS D:233 , HOH D:446BINDING SITE FOR RESIDUE EDO D 305
21CC3SOFTWAREGLY B:187 , LEU B:188 , HOH B:537 , LEU D:201 , ARG D:202BINDING SITE FOR RESIDUE EDO D 306
22CC4SOFTWARESER A:260 , SER A:261 , HOH A:580 , ALA C:119 , LYS C:120 , DG H:2BINDING SITE FOR RESIDUE ACT H 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4IBU)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IBU)

(-) 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:197
                                                                                                                                                                                                                                     
               SCOP domains d4ibua_ A: p53 tumor suppressor, DNA-binding domain                                                                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeee..........eeee....eeee.....eeeeee.........eeeeeeee............hhhhhhh............eeee.....eeee......eeeeee..........eeeeeee..............eeeeeeee.....eeeeeeeeeee..hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ibu A  96 SVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVCVCACPGRDRRREEENLRKK 292
                                   105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       


Chain B from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                      
               SCOP domains d4ibub_ B: p53 tumor suppressor, DNA-binding domain                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ................eee...........eeee....eeee.....eeeeee.........eeeeeeee.hhhhh........hhhhh............eee......eeee......eeeeee..........eeeeeee..............eeeeeeee.....eeeeeeeeeee..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ibu B  94 SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVCVCACPGRDRRREEENLRK 291
                                   103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283        


Chain C from PDB  Type:PROTEIN  Length:195
                                                                                                                                                                                                                                   
               SCOP domains d4ibuc_ C: p53 tumor suppressor, DNA-binding domain                                                                                                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eee...........eeee....eeee.....eeeeee.........eeeeeeee.hhhhh......hhhhhh.............eeee.....eeee......eeeeee..........eeeeeee..............eeeeeeee.....eeeeeeeeeee..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ibu C  96 SVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVCVCACPGRDRRREEENLR 290
                                   105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285     


Chain D from PDB  Type:PROTEIN  Length:196
                                                                                                                                                                                                                                    
               SCOP domains d4ibud_ D: p53 tumor suppressor, DNA-binding domain                                                                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eee...........eeee....eeee.....eeeeee.........eeeeeeee.hhhhh......hhhhhh.............eee......eeee......eeeeee..........eeeeeee..............eeeeeeee.....eeeeeeeeeee..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ibu D  95 SSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVCVCACPGRDRRREEENLR 290
                                   104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284      


Chain E from PDB  Type:DNA  Length:11
                                           
                 4ibu E   1 CGGGCATGCCC  11
                                    10 


Chain F from PDB  Type:DNA  Length:11
                                           
                 4ibu F   2 GGGCATGCCCG  12
                                    11 


Chain G from PDB  Type:DNA  Length:12
                                            
                 4ibu G   1 CGGGCATGCCCG  12
                                    10  


Chain H from PDB  Type:DNA  Length:12
                                            
                 4ibu H   1 CGGGCATGCCCG  12
                                    10
   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  (1, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (122, 122)

Asymmetric/Biological Unit(hide GO term definitions)

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  P53_HUMAN | P04637
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 Related Entries

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

UniProtKB/Swiss-Prot
        P53_HUMAN | P04637: 1a1u 1aie 1c26 1dt7 1gzh 1h26 1hs5 1jsp 1kzy 1ma3 1olg 1olh 1pes 1pet 1sae 1saf 1sak 1sal 1tsr 1tup 1uol 1xqh 1yc5 1ycq 1ycr 1ycs 2ac0 2ady 2ahi 2ata 2b3g 2bim 2bin 2bio 2bip 2biq 2f1x 2fej 2foj 2foo 2gs0 2h1l 2h2d 2h2f 2h4f 2h4h 2h4j 2h59 2j0z 2j10 2j11 2j1w 2j1x 2j1y 2j1z 2j20 2j21 2k8f 2l14 2ly4 2mej 2mwo 2mwp 2mwy 2mzd 2ocj 2pcx 2ruk 2vuk 2wgx 2x0u 2x0v 2x0w 2xwr 2ybg 2ydr 2z5s 2z5t 3d05 3d06 3d07 3d08 3d09 3d0a 3dab 3dac 3igk 3igl 3kmd 3kz8 3lw1 3oq5 3pdh 3q01 3q05 3q06 3sak 3tg5 3ts8 3zme 4agl 4agm 4agn 4ago 4agp 4agq 4buz 4bv2 4fz3 4hfz 4hje 4ibq 4ibs 4ibt 4ibv 4ibw 4iby 4ibz 4ijt 4kvp 4lo9 4loe 4lof 4mzi 4mzr 4qo1 4rp6 4rp7 4x34 4xr8 4zzj 5a7b 5ab9 5aba 5aoi 5aoj 5aok 5aol 5aom 5bua 5ecg 5g4m 5g4n 5g4o 5hou 5hp0 5hpd 5lap 5lgy 5un8

(-) Related Entries Specified in the PDB File

4ibq 4ibs 4ibt 4ibv 4ibw 4iby 4ibz 4ijt