[English] 日本語
Yorodumi
- PDB-4fbw: Crystal structure of an unfused Mre11-Nbs1 complex with two manga... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fbw
TitleCrystal structure of an unfused Mre11-Nbs1 complex with two manganese ions per active site
Components
  • DNA repair and telomere maintenance protein nbs1
  • DNA repair protein rad32
KeywordsHYDROLASE/PROTEIN BINDING / DNA double-strand break repair / Nuclease / Hydrolase / HYDROLASE-PROTEIN BINDING complex
Function / homology
Function and homology information


Cytosolic sensors of pathogen-associated DNA / DNA Damage/Telomere Stress Induced Senescence / HDR through MMEJ (alt-NHEJ) / Sensing of DNA Double Strand Breaks / Processing of DNA double-strand break ends / mitochondrial double-strand break repair via homologous recombination / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Mre11 complex / chromosome, telomeric repeat region / meiotic DNA double-strand break formation ...Cytosolic sensors of pathogen-associated DNA / DNA Damage/Telomere Stress Induced Senescence / HDR through MMEJ (alt-NHEJ) / Sensing of DNA Double Strand Breaks / Processing of DNA double-strand break ends / mitochondrial double-strand break repair via homologous recombination / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Mre11 complex / chromosome, telomeric repeat region / meiotic DNA double-strand break formation / phosphorylation-dependent protein binding / DNA end binding / Y-form DNA binding / double-strand break repair involved in meiotic recombination / chromatin-protein adaptor activity / DNA double-strand break processing / nuclease activity / single-stranded DNA endodeoxyribonuclease activity / double-stranded DNA 3'-5' DNA exonuclease activity / telomere maintenance via recombination / single-stranded DNA 3'-5' DNA exonuclease activity / reciprocal meiotic recombination / mitotic intra-S DNA damage checkpoint signaling / DNA duplex unwinding / protein localization to chromosome, telomeric region / mitotic G2 DNA damage checkpoint signaling / telomere maintenance / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / double-strand break repair / site of double-strand break / manganese ion binding / damaged DNA binding / molecular adaptor activity / Hydrolases; Acting on ester bonds / DNA repair / nucleus
Similarity search - Function
Mre11, capping domain / Nibrin-related / DNA double-strand break repair protein Mre11 / Mre11, DNA-binding / Mre11, capping domain / Mre11 DNA-binding presumed domain / Mre11 DNA-binding presumed domain / Mre11 nuclease, N-terminal metallophosphatase domain / Translation Initiation Factor IF3 / Metallo-dependent phosphatases ...Mre11, capping domain / Nibrin-related / DNA double-strand break repair protein Mre11 / Mre11, DNA-binding / Mre11, capping domain / Mre11 DNA-binding presumed domain / Mre11 DNA-binding presumed domain / Mre11 nuclease, N-terminal metallophosphatase domain / Translation Initiation Factor IF3 / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / SMAD/FHA domain superfamily / Metallo-dependent phosphatase-like / BRCT domain superfamily / 4-Layer Sandwich / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / DNA repair and telomere maintenance protein nbs1 / Double-strand break repair protein rad32
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSchiller, C.B. / Lammens, K. / Hopfner, K.P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structure of Mre11-Nbs1 complex yields insights into ataxia-telangiectasia-like disease mutations and DNA damage signaling.
Authors: Schiller, C.B. / Lammens, K. / Guerini, I. / Coordes, B. / Feldmann, H. / Schlauderer, F. / Mockel, C. / Schele, A. / Strasser, K. / Jackson, S.P. / Hopfner, K.P.
History
DepositionMay 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA repair protein rad32
B: DNA repair protein rad32
C: DNA repair and telomere maintenance protein nbs1
D: DNA repair and telomere maintenance protein nbs1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,9388
Polymers108,7184
Non-polymers2204
Water3,747208
1
A: DNA repair protein rad32
C: DNA repair and telomere maintenance protein nbs1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4694
Polymers54,3592
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-20 kcal/mol
Surface area18930 Å2
MethodPISA
2
B: DNA repair protein rad32
D: DNA repair and telomere maintenance protein nbs1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4694
Polymers54,3592
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-15 kcal/mol
Surface area19160 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7990 Å2
ΔGint-47 kcal/mol
Surface area35030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.122, 79.955, 220.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein DNA repair protein rad32


Mass: 47382.273 Da / Num. of mol.: 2 / Fragment: Mre11 amino acids 7-413
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: rad32, SPAC13C5.07 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09683
#2: Protein DNA repair and telomere maintenance protein nbs1


Mass: 6976.764 Da / Num. of mol.: 2 / Fragment: Nbs1 amino acids 474-531
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: nbs1, SPBC6B1.09c / Production host: Escherichia coli (E. coli) / References: UniProt: O43070
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growMethod: vapor diffusion, hanging drop
Details: 200 mM ammonium citrate pH 5.5 14 % PEG 3350 50 mM MnCl2, VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 10, 2009
RadiationMonochromator: Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.2→47.537 Å / Num. all: 53880 / Num. obs: 53880 / % possible obs: 99.37 % / Observed criterion σ(I): 3

-
Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→47.537 Å / SU ML: 0.28 / σ(F): 2 / Phase error: 24.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2439 2000 3.71 %Random
Rwork0.2331 ---
obs0.2335 53872 99.37 %-
all-53880 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.752 Å2 / ksol: 0.325 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.4285 Å2-0 Å20 Å2
2---3.135 Å20 Å2
3---1.7065 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6491 0 4 208 6703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146635
X-RAY DIFFRACTIONf_angle_d1.7668998
X-RAY DIFFRACTIONf_dihedral_angle_d16.0932486
X-RAY DIFFRACTIONf_chiral_restr0.125999
X-RAY DIFFRACTIONf_plane_restr0.0081174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1996-2.25460.31341310.2983421X-RAY DIFFRACTION94
2.2546-2.31550.31391400.28823599X-RAY DIFFRACTION98
2.3155-2.38370.28971410.27553679X-RAY DIFFRACTION100
2.3837-2.46060.31430.26683685X-RAY DIFFRACTION100
2.4606-2.54850.28091420.27483682X-RAY DIFFRACTION100
2.5485-2.65060.29171420.27193676X-RAY DIFFRACTION100
2.6506-2.77120.27481410.26123693X-RAY DIFFRACTION100
2.7712-2.91730.31421440.26683711X-RAY DIFFRACTION100
2.9173-3.10.2811440.25373734X-RAY DIFFRACTION100
3.1-3.33930.26411420.2473710X-RAY DIFFRACTION100
3.3393-3.67530.2741450.22253738X-RAY DIFFRACTION100
3.6753-4.20680.19711440.20113756X-RAY DIFFRACTION100
4.2068-5.2990.17731470.18373811X-RAY DIFFRACTION100
5.299-47.54850.21871540.23243977X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -25.8655 Å / Origin y: 0.5014 Å / Origin z: -30.2657 Å
111213212223313233
T0.1026 Å20.0172 Å2-0.0583 Å2-0.0752 Å2-0.078 Å2--0.1032 Å2
L0.6194 °20.2515 °20.2574 °2-0.6427 °2-0.1199 °2--0.3583 °2
S0.0358 Å °-0.1222 Å °0.0385 Å °0.074 Å °-0.036 Å °-0.0272 Å °-0.069 Å °-0.0545 Å °0.0306 Å °
Refinement TLS groupSelection details: all

+
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://pdbjlvh1.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