[English] 日本語
Yorodumi
- PDB-4nb3: Crystal structure of RPA70N in complex with a 3,4 dichlorophenyla... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nb3
TitleCrystal structure of RPA70N in complex with a 3,4 dichlorophenylalanine ATRIP derived peptide
Components
  • 3,4 dichlorophenylalanine ATRIP derived peptide
  • Replication protein A 70 kDa DNA-binding subunit
KeywordsPEPTIDE BINDING PROTEIN / OB fold / Protein-Protein Interaction / 3 / 4 dichlorophenylalanine
Function / homology
Function and homology information


ATR-ATRIP complex / protein localization to chromosome / DNA replication factor A complex / single-stranded telomeric DNA binding / chromatin-protein adaptor activity / G-rich strand telomeric DNA binding / protein localization to site of double-strand break / Removal of the Flap Intermediate / regulation of double-strand break repair / Removal of the Flap Intermediate from the C-strand ...ATR-ATRIP complex / protein localization to chromosome / DNA replication factor A complex / single-stranded telomeric DNA binding / chromatin-protein adaptor activity / G-rich strand telomeric DNA binding / protein localization to site of double-strand break / Removal of the Flap Intermediate / regulation of double-strand break repair / Removal of the Flap Intermediate from the C-strand / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / nucleobase-containing compound metabolic process / HDR through Single Strand Annealing (SSA) / K63-linked polyubiquitin modification-dependent protein binding / Impaired BRCA2 binding to RAD51 / site of DNA damage / Presynaptic phase of homologous DNA pairing and strand exchange / PCNA-Dependent Long Patch Base Excision Repair / Activation of the pre-replicative complex / Regulation of HSF1-mediated heat shock response / HSF1 activation / telomere maintenance via telomerase / mismatch repair / SUMOylation of DNA damage response and repair proteins / Activation of ATR in response to replication stress / telomere maintenance / DNA damage checkpoint signaling / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / meiotic cell cycle / nucleotide-excision repair / Fanconi Anemia Pathway / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / double-strand break repair via homologous recombination / Translesion Synthesis by POLH / G2/M DNA damage checkpoint / base-excision repair / PML body / Meiotic recombination / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / DNA-templated DNA replication / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / single-stranded DNA binding / site of double-strand break / Processing of DNA double-strand break ends / DNA recombination / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / chromosome, telomeric region / DNA replication / DNA repair / DNA damage response / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
ATR-interacting protein / Replication factor-A protein 1, N-terminal domain / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / : / Replication factor A, C-terminal / Replication factor-A C terminal domain / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type ...ATR-interacting protein / Replication factor-A protein 1, N-terminal domain / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / : / Replication factor A, C-terminal / Replication factor-A C terminal domain / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Replication protein A 70 kDa DNA-binding subunit / ATR-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsFeldkamp, M.D. / Frank, A.O. / Vangamudi, B. / Souza-Fagundes, E.M. / Luzwik, J.W. / Cortez, D. / Olejniczak, O.T. / Waterson, A.G. / Rossanese, O.W. / Fesik, S.W. / Chazin, W.J.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Discovery of a Potent Stapled Helix Peptide That Binds to the 70N Domain of Replication Protein A.
Authors: Frank, A.O. / Vangamudi, B. / Feldkamp, M.D. / Souza-Fagundes, E.M. / Luzwick, J.W. / Cortez, D. / Olejniczak, E.T. / Waterson, A.G. / Rossanese, O.W. / Chazin, W.J. / Fesik, S.W.
History
DepositionOct 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.0Jul 10, 2024Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Replication protein A 70 kDa DNA-binding subunit
B: Replication protein A 70 kDa DNA-binding subunit
C: 3,4 dichlorophenylalanine ATRIP derived peptide
D: 3,4 dichlorophenylalanine ATRIP derived peptide


Theoretical massNumber of molelcules
Total (without water)31,4284
Polymers31,4284
Non-polymers00
Water8,161453
1
A: Replication protein A 70 kDa DNA-binding subunit
C: 3,4 dichlorophenylalanine ATRIP derived peptide


Theoretical massNumber of molelcules
Total (without water)15,7142
Polymers15,7142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Replication protein A 70 kDa DNA-binding subunit
D: 3,4 dichlorophenylalanine ATRIP derived peptide


Theoretical massNumber of molelcules
Total (without water)15,7142
Polymers15,7142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.145, 46.803, 78.792
Angle α, β, γ (deg.)90.00, 120.64, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-396-

HOH

-
Components

#1: Protein Replication protein A 70 kDa DNA-binding subunit / RP-A p70 / Replication factor A protein 1 / RF-A protein 1 / Single-stranded DNA-binding protein / ...RP-A p70 / Replication factor A protein 1 / RF-A protein 1 / Single-stranded DNA-binding protein / Replication protein A 70 kDa DNA-binding subunit / N-terminally processed


Mass: 13497.728 Da / Num. of mol.: 2 / Mutation: E7R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPA1, REPA1, RPA70 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P27694
#2: Protein/peptide 3,4 dichlorophenylalanine ATRIP derived peptide


Mass: 2216.161 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Synthesized peptide contains a covalently attached fluorescein isothiocyanate (FITC) at its N-terminus and a 3,4 dichlorophenylalanine incorporated into the peptide chain at position 15
References: UniProt: Q8WXE1*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM Bis-Tris, 200 mM ammonium acetate, 25% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.35→26.17 Å / Num. obs: 60645 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Net I/σ(I): 11.57
Reflection shellResolution: 1.35→1.4 Å / % possible all: 91.2

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.8.2_1309)model building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.2_1309phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4PIC

4pic


Resolution: 1.35→26.17 Å / SU ML: 0.11 / σ(F): 1.35 / Phase error: 15.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1747 3095 5.1 %RANDOM
Rwork0.1442 ---
obs0.1457 60645 97.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→26.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2171 0 0 453 2624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182454
X-RAY DIFFRACTIONf_angle_d1.9353385
X-RAY DIFFRACTIONf_dihedral_angle_d15.5861007
X-RAY DIFFRACTIONf_chiral_restr0.127388
X-RAY DIFFRACTIONf_plane_restr0.01438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.37170.23781270.17622463X-RAY DIFFRACTION91
1.3717-1.39420.21641430.16832626X-RAY DIFFRACTION100
1.3942-1.41820.20171330.15622705X-RAY DIFFRACTION100
1.4182-1.4440.24781380.15212643X-RAY DIFFRACTION100
1.444-1.47180.18331470.1472655X-RAY DIFFRACTION100
1.4718-1.50180.16971580.13552677X-RAY DIFFRACTION100
1.5018-1.53450.2071250.12692666X-RAY DIFFRACTION100
1.5345-1.57020.17541600.12022644X-RAY DIFFRACTION100
1.5702-1.60940.18331570.12272684X-RAY DIFFRACTION100
1.6094-1.65290.15811330.11732644X-RAY DIFFRACTION100
1.6529-1.70160.17011380.12192701X-RAY DIFFRACTION100
1.7016-1.75650.14871660.12572663X-RAY DIFFRACTION100
1.7565-1.81920.20091350.13012662X-RAY DIFFRACTION100
1.8192-1.89210.18051360.13642681X-RAY DIFFRACTION100
1.8921-1.97810.16671560.13712596X-RAY DIFFRACTION98
1.9781-2.08240.15451580.1322661X-RAY DIFFRACTION100
2.0824-2.21280.16471370.14272715X-RAY DIFFRACTION100
2.2128-2.38350.17461320.14242562X-RAY DIFFRACTION95
2.3835-2.62320.17261440.14812690X-RAY DIFFRACTION100
2.6232-3.00230.18211280.15992731X-RAY DIFFRACTION100
3.0023-3.78080.16831220.1442308X-RAY DIFFRACTION87
3.7808-26.17480.1751220.16092173X-RAY DIFFRACTION95

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more