Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  HUMAN RAD51 POST-SYNAPTIC COMPLEXES
 
Authors :  J. Xu, L. Zhao, Y. Xu, W. Zhao, P. Sung, H. W. Wang
Date :  08 Oct 16  (Deposition) - 21 Dec 16  (Release) - 25 Jan 17  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  4.50
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Dna Repair, Atpase, Homologous Recombination, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Xu, L. Zhao, Y. Xu, W. Zhao, P. Sung, H. W. Wang
Cryo-Em Structures Of Human Rad51 Recombinase Filaments During Catalysis Of Dna-Strand Exchange
Nat. Struct. Mol. Biol. V. 24 40 2017
PubMed-ID: 27941862  |  Reference-DOI: 10.1038/NSMB.3336

(-) Compounds

Molecule 1 - DNA REPAIR PROTEIN RAD51 HOMOLOG 1
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'
    Expression System Taxid: 866768
    Gene: RAD51, RAD51A, RECA
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HRAD51,RAD51 HOMOLOG A
 
Molecule 2 - DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
    Chains: D
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
    Chains: E
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1ANP3Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG3Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:134 , ASP A:222 , ANP A:602binding site for residue MG A 601
2AC2SOFTWAREARG A:130 , THR A:131 , GLY A:132 , LYS A:133 , THR A:134 , GLN A:135 , GLU A:163 , ARG A:170 , GLN A:268 , ARG A:310 , MG A:601 , HIS B:294 , SER B:296 , ASP B:316 , SER B:317 , PRO B:318 , CYS B:319 , LEU B:320 , PRO B:321binding site for residue ANP A 602
3AC3SOFTWARETHR B:134 , ASP B:222 , ANP B:602binding site for residue MG B 601
4AC4SOFTWAREARG B:130 , THR B:131 , GLY B:132 , LYS B:133 , THR B:134 , GLN B:135 , GLU B:163 , ARG B:170 , GLN B:268 , ARG B:310 , MG B:601 , HIS C:294 , SER C:296 , ASP C:316 , SER C:317 , PRO C:318 , CYS C:319 , LEU C:320 , PRO C:321binding site for residue ANP B 602
5AC5SOFTWAREARG C:130 , THR C:131 , GLY C:132 , LYS C:133 , THR C:134 , GLN C:135 , GLU C:163 , ARG C:170 , GLN C:268 , ARG C:310 , MG C:402binding site for residue ANP C 401
6AC6SOFTWARETHR C:134 , ASP C:222 , ANP C:401binding site for residue MG C 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5H1C)

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1Gly A:234 -Arg A:235
2Arg A:235 -Gly A:236
3Gly A:236 -Glu A:237
4Gly B:234 -Arg B:235
5Arg B:235 -Gly B:236
6Gly B:236 -Glu B:237
7Gly C:234 -Arg C:235
8Arg C:235 -Gly C:236
9Gly C:236 -Glu C:237

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5H1C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5H1C)

(-) Exons   (0, 0)

(no "Exon" information available for 5H1C)

(-) 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:311
                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh....hhhhhhhhhhhh..hhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhh.....hhhhhhhhhh........hhhhhhhh........eeeee.....hhhhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhh.hhhhhhhh.eeee....hhhhhhhhhhhhhhh...eeeeee...hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..eeeee................hhhhhhhhh..eeeeee.....eeeeee........eeee.ee..ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h1c A  22 PQPISRLEQCGINANDVKKLEEAGFHTVEAVAYAPKKELINIKGISEAKADKILAEAAKLVPMGFTTATEFHQRRSEIIQITTGSKELDKLLQGGIETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERLLAVAERYGLSGSDVLDNVAYARAFNTDHQTQLLYQASAMMVESRYALLIVDSATALYRTDYSGRGELSARQMHLARFLRMLLRLADEFGVAVVITNQVVAQVDGAADPKKPIGGNIIAHASTTRLYLRKGRGETRICQIYDSPCLPEAEAMFAINADGVGD 336
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271     ||285       295       305       315       325       335 
                                                                                                                                                                                                                                                                                         277|                                                      
                                                                                                                                                                                                                                                                                          282                                                      


Chain B from PDB  Type:PROTEIN  Length:311
                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh....hhhhhhhhhhhh..hhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhh....eehhhhhhhhh........hhhhhhhh........eeeee.....hhhhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhh.hhhhhhhh.eeee....hhhhhhhhhhhhhhh...eeeeee...hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..eeeee................hhhhhhhhh..eeeeee.....eeeeee........eeee.ee..ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h1c B  22 PQPISRLEQCGINANDVKKLEEAGFHTVEAVAYAPKKELINIKGISEAKADKILAEAAKLVPMGFTTATEFHQRRSEIIQITTGSKELDKLLQGGIETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERLLAVAERYGLSGSDVLDNVAYARAFNTDHQTQLLYQASAMMVESRYALLIVDSATALYRTDYSGRGELSARQMHLARFLRMLLRLADEFGVAVVITNQVVAQVDGAADPKKPIGGNIIAHASTTRLYLRKGRGETRICQIYDSPCLPEAEAMFAINADGVGD 336
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271     ||285       295       305       315       325       335 
                                                                                                                                                                                                                                                                                         277|                                                      
                                                                                                                                                                                                                                                                                          282                                                      


Chain C from PDB  Type:PROTEIN  Length:311
                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh....hhhhhhhhhhhh..hhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhh....eehhhhhhhhh........hhhhhhhh........eeeee.....hhhhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhh.hhhhhhhh.eeee....hhhhhhhhhhhhhhh...eeeeee...hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..eeeee................hhhhhhhhh..eeeeee.....eeeeee........eeee.ee..ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h1c C  22 PQPISRLEQCGINANDVKKLEEAGFHTVEAVAYAPKKELINIKGISEAKADKILAEAAKLVPMGFTTATEFHQRRSEIIQITTGSKELDKLLQGGIETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERLLAVAERYGLSGSDVLDNVAYARAFNTDHQTQLLYQASAMMVESRYALLIVDSATALYRTDYSGRGELSARQMHLARFLRMLLRLADEFGVAVVITNQVVAQVDGAADPKKPIGGNIIAHASTTRLYLRKGRGETRICQIYDSPCLPEAEAMFAINADGVGD 336
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271     ||285       295       305       315       325       335 
                                                                                                                                                                                                                                                                                         277|                                                      
                                                                                                                                                                                                                                                                                          282                                                      


Chain D from PDB  Type:DNA  Length:9
                                         
                 5h1c D   1 TTTTTTTTT   9


Chain E from PDB  Type:DNA  Length:9
                                         
                 5h1c E   1 AAAAAAAAA   9
   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 5H1C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5H1C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5H1C)

(-) Gene Ontology  (67, 67)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ANP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:235 - Gly A:236   [ RasMol ]  
    Arg B:235 - Gly B:236   [ RasMol ]  
    Arg C:235 - Gly C:236   [ RasMol ]  
    Gly A:234 - Arg A:235   [ RasMol ]  
    Gly A:236 - Glu A:237   [ RasMol ]  
    Gly B:234 - Arg B:235   [ RasMol ]  
    Gly B:236 - Glu B:237   [ RasMol ]  
    Gly C:234 - Arg C:235   [ RasMol ]  
    Gly C:236 - Glu C:237   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5h1c
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  RAD51_HUMAN | Q06609
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  RAD51_HUMAN | Q06609
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        RAD51_HUMAN | Q06609: 1b22 1n0w 5h1b 5jzc 5np7

(-) Related Entries Specified in the PDB File

5h1b