5H1C

Human RAD51 post-synaptic complexes

> Summary

Summary for 5H1C

Related5H1B
EMDB informationEMD-9567 EMD-9568 EMD-9566
DescriptorDNA repair protein RAD51 homolog 1/DNA Complex
Functional Keywordsdna repair, atpase, homologous recombination, dna binding protein-dna complex, dna binding protein/dna
Biological sourceHomo sapiens (Human)
More
Cellular locationNucleus  Q06609
Total number of polymer chains5
Total molecular weight118082.41
Authors
Xu, J.,Zhao, L.,Xu, Y.,Zhao, W.,Sung, P.,Wang, H.W. (deposition date: 2016-10-08, release date: 2016-12-21, modification date: 2017-01-25)
Primary citation
Xu, J.,Zhao, L.,Xu, Y.,Zhao, W.,Sung, P.,Wang, H.W.
Cryo-EM structures of human RAD51 recombinase filaments during catalysis of DNA-strand exchange
Nat. Struct. Mol. Biol., 24:40-46, 2017
PubMed: 27941862
DOI: 10.1038/nsmb.3336
MImport into Mendeley
Experimental method
ELECTRON MICROSCOPY
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Structure validation

ClashscoreRamachandran outliersSidechain outliers412.3%4.8%MetricValuePercentile RanksWorseBetterPercentile relative to all structuresPercentile relative to all EM structures

More Asymmetric unit images

Molmil generated image of 5h1c
no rotation
Molmil generated image of 5h1c
rotated about x axis by 90°
Molmil generated image of 5h1c
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, B, CDNA repair protein RAD51 homolog 1polymer33937008.13
UniProt (Q06609)
Pfam (PF08423)
Pfam (PF14520)
Homo sapiens (Human)hRAD51,RAD51 homolog A
DDNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')polymer92692.81
Homo sapiens
EDNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')polymer92773.91
Homo sapiens
MAGNESIUM IONnon-polymer24.33
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTERnon-polymer506.23

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains5
Total molecular weight116490.9
Non-Polymers*Number of molecules6
Total molecular weight1591.5
All*Total molecular weight118082.4
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:ELECTRON MICROSCOPY

Resolution limits -
the highest resolution shell value -

Data Collection Statistics

Resolution limits -
the highest resolution shell value -

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0000785cellular_componentchromatin
A0000793cellular_componentcondensed chromosome
A0000794cellular_componentcondensed nuclear chromosome
A0005737cellular_componentcytoplasm
A0005829cellular_componentcytosol
A0000800cellular_componentlateral element
A0005815cellular_componentmicrotubule organizing center
A0005759cellular_componentmitochondrial matrix
A0005739cellular_componentmitochondrion
A0000790cellular_componentnuclear chromatin
A0000228cellular_componentnuclear chromosome
A0000784cellular_componentnuclear chromosome, telomeric region
A0005730cellular_componentnucleolus
A0005654cellular_componentnucleoplasm
A0005634cellular_componentnucleus
A0048471cellular_componentperinuclear region of cytoplasm
A0016605cellular_componentPML body
A0035861cellular_componentsite of double-strand break
A0005524molecular_functionATP binding
A0003682molecular_functionchromatin binding
A0070182molecular_functionDNA polymerase binding
A0003690molecular_functiondouble-stranded DNA binding
A0000400molecular_functionfour-way junction DNA binding
A0042802molecular_functionidentical protein binding
A0008022molecular_functionprotein C-terminus binding
A0000150molecular_functionrecombinase activity
A0003697molecular_functionsingle-stranded DNA binding
A0043142molecular_functionsingle-stranded DNA-dependent ATPase activity
A0072757biological_processcellular response to camptothecin
A0072719biological_processcellular response to cisplatin
A0006974biological_processcellular response to DNA damage stimulus
A0071480biological_processcellular response to gamma radiation
A0072711biological_processcellular response to hydroxyurea
A0071479biological_processcellular response to ionizing radiation
A0070192biological_processchromosome organization involved in meiotic cell cycle
A0000730biological_processDNA recombinase assembly
A0006310biological_processDNA recombination
A0006281biological_processDNA repair
A0000731biological_processDNA synthesis involved in DNA repair
A0006268biological_processDNA unwinding involved in DNA replication
A0000724biological_processdouble-strand break repair via homologous recombination
A0036297biological_processinterstrand cross-link repair
A0007126biological_processmeiotic nuclear division
A0006312biological_processmitotic recombination
A1990426biological_processmitotic recombination-dependent replication fork processing
A0051106biological_processpositive regulation of DNA ligation
A0051260biological_processprotein homooligomerization
A0007131biological_processreciprocal meiotic recombination
A0010569biological_processregulation of double-strand break repair via homologous recombination
A0001932biological_processregulation of protein phosphorylation
A0031297biological_processreplication fork processing
A1990414biological_processreplication-born double-strand break repair via sister chromatid exchange
A0042493biological_processresponse to drug
A1904631biological_processresponse to glucoside
A0009636biological_processresponse to toxic substance
A0010165biological_processresponse to X-ray
A0000732biological_processstrand displacement
A0042148biological_processstrand invasion
A0000722biological_processtelomere maintenance via recombination
A0010833biological_processtelomere maintenance via telomere lengthening
B0000785cellular_componentchromatin
B0000793cellular_componentcondensed chromosome
B0000794cellular_componentcondensed nuclear chromosome
B0005737cellular_componentcytoplasm
B0005829cellular_componentcytosol
B0000800cellular_componentlateral element
B0005815cellular_componentmicrotubule organizing center
B0005759cellular_componentmitochondrial matrix
B0005739cellular_componentmitochondrion
B0000790cellular_componentnuclear chromatin
B0000228cellular_componentnuclear chromosome
B0000784cellular_componentnuclear chromosome, telomeric region
B0005730cellular_componentnucleolus
B0005654cellular_componentnucleoplasm
B0005634cellular_componentnucleus
B0048471cellular_componentperinuclear region of cytoplasm
B0016605cellular_componentPML body
B0035861cellular_componentsite of double-strand break
B0005524molecular_functionATP binding
B0003682molecular_functionchromatin binding
B0070182molecular_functionDNA polymerase binding
B0003690molecular_functiondouble-stranded DNA binding
B0000400molecular_functionfour-way junction DNA binding
B0042802molecular_functionidentical protein binding
B0008022molecular_functionprotein C-terminus binding
B0000150molecular_functionrecombinase activity
B0003697molecular_functionsingle-stranded DNA binding
B0043142molecular_functionsingle-stranded DNA-dependent ATPase activity
B0072757biological_processcellular response to camptothecin
B0072719biological_processcellular response to cisplatin
B0006974biological_processcellular response to DNA damage stimulus
B0071480biological_processcellular response to gamma radiation
B0072711biological_processcellular response to hydroxyurea
B0071479biological_processcellular response to ionizing radiation
B0070192biological_processchromosome organization involved in meiotic cell cycle
B0000730biological_processDNA recombinase assembly
B0006310biological_processDNA recombination
B0006281biological_processDNA repair
B0000731biological_processDNA synthesis involved in DNA repair
B0006268biological_processDNA unwinding involved in DNA replication
B0000724biological_processdouble-strand break repair via homologous recombination
B0036297biological_processinterstrand cross-link repair
B0007126biological_processmeiotic nuclear division
B0006312biological_processmitotic recombination
B1990426biological_processmitotic recombination-dependent replication fork processing
B0051106biological_processpositive regulation of DNA ligation
B0051260biological_processprotein homooligomerization
B0007131biological_processreciprocal meiotic recombination
B0010569biological_processregulation of double-strand break repair via homologous recombination
B0001932biological_processregulation of protein phosphorylation
B0031297biological_processreplication fork processing
B1990414biological_processreplication-born double-strand break repair via sister chromatid exchange
B0042493biological_processresponse to drug
B1904631biological_processresponse to glucoside
B0009636biological_processresponse to toxic substance
B0010165biological_processresponse to X-ray
B0000732biological_processstrand displacement
B0042148biological_processstrand invasion
B0000722biological_processtelomere maintenance via recombination
B0010833biological_processtelomere maintenance via telomere lengthening
C0000785cellular_componentchromatin
C0000793cellular_componentcondensed chromosome
C0000794cellular_componentcondensed nuclear chromosome
C0005737cellular_componentcytoplasm
C0005829cellular_componentcytosol
C0000800cellular_componentlateral element
C0005815cellular_componentmicrotubule organizing center
C0005759cellular_componentmitochondrial matrix
C0005739cellular_componentmitochondrion
C0000790cellular_componentnuclear chromatin
C0000228cellular_componentnuclear chromosome
C0000784cellular_componentnuclear chromosome, telomeric region
C0005730cellular_componentnucleolus
C0005654cellular_componentnucleoplasm
C0005634cellular_componentnucleus
C0048471cellular_componentperinuclear region of cytoplasm
C0016605cellular_componentPML body
C0035861cellular_componentsite of double-strand break
C0005524molecular_functionATP binding
C0003682molecular_functionchromatin binding
C0070182molecular_functionDNA polymerase binding
C0003690molecular_functiondouble-stranded DNA binding
C0000400molecular_functionfour-way junction DNA binding
C0042802molecular_functionidentical protein binding
C0008022molecular_functionprotein C-terminus binding
C0000150molecular_functionrecombinase activity
C0003697molecular_functionsingle-stranded DNA binding
C0043142molecular_functionsingle-stranded DNA-dependent ATPase activity
C0072757biological_processcellular response to camptothecin
C0072719biological_processcellular response to cisplatin
C0006974biological_processcellular response to DNA damage stimulus
C0071480biological_processcellular response to gamma radiation
C0072711biological_processcellular response to hydroxyurea
C0071479biological_processcellular response to ionizing radiation
C0070192biological_processchromosome organization involved in meiotic cell cycle
C0000730biological_processDNA recombinase assembly
C0006310biological_processDNA recombination
C0006281biological_processDNA repair
C0000731biological_processDNA synthesis involved in DNA repair
C0006268biological_processDNA unwinding involved in DNA replication
C0000724biological_processdouble-strand break repair via homologous recombination
C0036297biological_processinterstrand cross-link repair
C0007126biological_processmeiotic nuclear division
C0006312biological_processmitotic recombination
C1990426biological_processmitotic recombination-dependent replication fork processing
C0051106biological_processpositive regulation of DNA ligation
C0051260biological_processprotein homooligomerization
C0007131biological_processreciprocal meiotic recombination
C0010569biological_processregulation of double-strand break repair via homologous recombination
C0001932biological_processregulation of protein phosphorylation
C0031297biological_processreplication fork processing
C1990414biological_processreplication-born double-strand break repair via sister chromatid exchange
C0042493biological_processresponse to drug
C1904631biological_processresponse to glucoside
C0009636biological_processresponse to toxic substance
C0010165biological_processresponse to X-ray
C0000732biological_processstrand displacement
C0042148biological_processstrand invasion
C0000722biological_processtelomere maintenance via recombination
C0010833biological_processtelomere maintenance via telomere lengthening
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC13binding site for residue MG A 601
ChainResidue
ATHR134
AASP222
AANP602

AC219binding site for residue ANP A 602
ChainResidue
AARG130
ATHR131
AGLY132
ALYS133
ATHR134
AGLN135
AGLU163
AARG170
AGLN268
AARG310
AMG601
BHIS294
BSER296
BASP316
BSER317
BPRO318
BCYS319
BLEU320
BPRO321

AC33binding site for residue MG B 601
ChainResidue
BTHR134
BASP222
BANP602

AC419binding site for residue ANP B 602
ChainResidue
BARG130
BTHR131
BGLY132
BLYS133
BTHR134
BGLN135
BGLU163
BARG170
BGLN268
BARG310
BMG601
CHIS294
CSER296
CASP316
CSER317
CPRO318
CCYS319
CLEU320
CPRO321

AC511binding site for residue ANP C 401
ChainResidue
CARG130
CTHR131
CGLY132
CLYS133
CTHR134
CGLN135
CGLU163
CARG170
CGLN268
CARG310
CMG402

AC63binding site for residue MG C 402
ChainResidue
CTHR134
CASP222
CANP401

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
ANP_5h1c_A_60228PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER binding site
ChainResidueligand
APHE129-GLN135ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
AGLU163ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ATHR165ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
AARG170ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
AASP222ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
AGLN268ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
AGLU308ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
AARG310ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
AILE329-ASN330ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
BALA293-THR297ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
BASP316-GLU322ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

ANP_5h1c_B_60228PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER binding site
ChainResidueligand
BPHE129-GLN135ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
BGLU163ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
BTHR165ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
BARG170ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
BASP222ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
BGLN268ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
BGLU308ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
BARG310ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
BILE329-ASN330ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
CALA293-THR297ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
CASP316-GLU322ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

ANP_5h1c_C_40116PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER binding site
ChainResidueligand
CPHE129-GLN135ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
CGLU163ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
CTHR165ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
CARG170ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
CASP222ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
CGLN268ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
CGLU308ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
CARG310ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
CILE329-ASN330ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI11ATP. {ECO:0000250}.
ChainResidueDetails
AGLY127-THR134

SWS_FT_FI21ATP. {ECO:0000250}.
ChainResidueDetails
BGLY127-THR134

SWS_FT_FI31ATP. {ECO:0000250}.
ChainResidueDetails
CGLY127-THR134

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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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