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- PDB-4cvo: Crystal structure of the N-terminal colied-coil domain of human D... -

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Basic information

Entry
Database: PDB / ID: 4cvo
TitleCrystal structure of the N-terminal colied-coil domain of human DNA excision repair protein ERCC-6
ComponentsDNA EXCISION REPAIR PROTEIN ERCC-6
KeywordsHYDROLASE / COCKAYNE SYNDROME / NUCLEOTIDE EXCISION REPAIR
Function / homology
Function and homology information


negative regulation of double-strand break repair via nonhomologous end joining / regulation of transcription elongation by RNA polymerase II / DNA protection / single strand break repair / B-WICH complex / response to superoxide / double-strand break repair via classical nonhomologous end joining / photoreceptor cell maintenance / RNA polymerase binding / positive regulation of DNA-templated transcription, elongation ...negative regulation of double-strand break repair via nonhomologous end joining / regulation of transcription elongation by RNA polymerase II / DNA protection / single strand break repair / B-WICH complex / response to superoxide / double-strand break repair via classical nonhomologous end joining / photoreceptor cell maintenance / RNA polymerase binding / positive regulation of DNA-templated transcription, elongation / chromatin-protein adaptor activity / response to UV-B / ATP-dependent chromatin remodeler activity / positive regulation of transcription by RNA polymerase III / ATP-dependent DNA damage sensor activity / positive regulation of transcription by RNA polymerase I / RNA Polymerase I Transcription Initiation / protein tyrosine kinase activator activity / pyrimidine dimer repair / positive regulation of transcription initiation by RNA polymerase II / response to X-ray / ATP-dependent activity, acting on DNA / transcription elongation by RNA polymerase I / positive regulation of double-strand break repair via homologous recombination / site of DNA damage / JNK cascade / protein localization to chromatin / transcription-coupled nucleotide-excision repair / neurogenesis / DNA damage checkpoint signaling / regulation of DNA-templated transcription elongation / positive regulation of DNA repair / transcription elongation factor complex / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / helicase activity / response to gamma radiation / base-excision repair / B-WICH complex positively regulates rRNA expression / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / multicellular organism growth / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / intrinsic apoptotic signaling pathway in response to DNA damage / response to toxic substance / Formation of TC-NER Pre-Incision Complex / neuron differentiation / neuron projection development / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / response to oxidative stress / transcription by RNA polymerase II / chromatin remodeling / DNA repair / chromatin binding / nucleolus / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
: / : / Rad26/CSB winged helix DNA-binding domain / : / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain ...: / : / Rad26/CSB winged helix DNA-binding domain / : / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA excision repair protein ERCC-6
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsNewman, J.A. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.
CitationJournal: To be Published
Title: Crystal Structure of the N-Terminal Colied-Coil Domain of Human DNA Excision Repair Protein Ercc-6
Authors: Newman, J.A. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.
History
DepositionMar 28, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA EXCISION REPAIR PROTEIN ERCC-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7882
Polymers8,7641
Non-polymers241
Water48627
1
A: DNA EXCISION REPAIR PROTEIN ERCC-6
hetero molecules

A: DNA EXCISION REPAIR PROTEIN ERCC-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5764
Polymers17,5272
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_875-x+3,-y+2,z1
Buried area910 Å2
ΔGint-14.5 kcal/mol
Surface area12180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.444, 37.444, 321.268
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-1159-

MG

21A-2003-

HOH

31A-2004-

HOH

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Components

#1: Protein DNA EXCISION REPAIR PROTEIN ERCC-6 / ATP-DEPENDENT HELICASE ERCC6 / COCKAYNE SYNDROME PROTEIN CSB


Mass: 8763.654 Da / Num. of mol.: 1 / Fragment: N-TERMINAL COIED-COIL DOMAIN, RESIDUES 84-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q03468, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsFIRST TWO RESIDUES REMAIN AFTER CLEAVAGE OF PURIFICATION TAG

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.71 Å3/Da / Density % sol: 66.84 % / Description: NONE
Crystal growDetails: 1.6 M MAGNESIUM SULFATE, 0.1 M MES PH 6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.85→45.9 Å / Num. obs: 12739 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 38.78 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.3
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 10.4 % / Rmerge(I) obs: 1.15 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→35.696 Å / SU ML: 0.25 / σ(F): 0.1 / Phase error: 28.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2553 1051 4.9 %
Rwork0.2364 --
obs0.2373 12582 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.03 Å2
Refinement stepCycle: LAST / Resolution: 1.85→35.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms520 0 1 27 548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007523
X-RAY DIFFRACTIONf_angle_d0.925710
X-RAY DIFFRACTIONf_dihedral_angle_d13.122188
X-RAY DIFFRACTIONf_chiral_restr0.03690
X-RAY DIFFRACTIONf_plane_restr0.00394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8501-1.93430.34751250.32422526X-RAY DIFFRACTION100
1.9343-2.03630.31011280.29172541X-RAY DIFFRACTION99
2.0363-2.16390.24651210.23862577X-RAY DIFFRACTION100
2.1639-2.33090.22991250.19362571X-RAY DIFFRACTION100
2.3309-2.56540.181200.2122531X-RAY DIFFRACTION100
2.5654-2.93650.23361560.22582538X-RAY DIFFRACTION100
2.9365-3.6990.26211290.25182562X-RAY DIFFRACTION100
3.699-35.70310.26881470.23252550X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 40.6334 Å / Origin y: 27.8008 Å / Origin z: 37.3129 Å
111213212223313233
T0.6256 Å20.4122 Å2-0.0479 Å2-0.7935 Å2-0.0072 Å2--0.5126 Å2
L1.5057 °20.4868 °20.955 °2-1.6127 °20.041 °2--1.7471 °2
S-0.1303 Å °0.1349 Å °0.2482 Å °-0.4376 Å °0.1314 Å °0.2012 Å °-0.9251 Å °-0.0846 Å °-0.3212 Å °
Refinement TLS groupSelection details: ALL

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