[English] 日本語
Yorodumi
- PDB-4day: Crystal structure of the RMI core complex with MM2 peptide from FANCM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4day
TitleCrystal structure of the RMI core complex with MM2 peptide from FANCM
Components
  • Fanconi anemia group M protein
  • RecQ-mediated genome instability protein 1
  • RecQ-mediated genome instability protein 2
Keywordsprotein binding/Hydrolase / OB fold / protein binding-Hydrolase complex
Function / homology
Function and homology information


regulation of sister chromatid segregation / double-strand break repair via synthesis-dependent strand annealing / RecQ family helicase-topoisomerase III complex / FANCM-MHF complex / reduction of food intake in response to dietary excess / resolution of DNA recombination intermediates / Fanconi anaemia nuclear complex / maintenance of rDNA / resolution of meiotic recombination intermediates / four-way junction helicase activity ...regulation of sister chromatid segregation / double-strand break repair via synthesis-dependent strand annealing / RecQ family helicase-topoisomerase III complex / FANCM-MHF complex / reduction of food intake in response to dietary excess / resolution of DNA recombination intermediates / Fanconi anaemia nuclear complex / maintenance of rDNA / resolution of meiotic recombination intermediates / four-way junction helicase activity / nuclease activity / Impaired BRCA2 binding to PALB2 / positive regulation of protein monoubiquitination / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / 3'-5' DNA helicase activity / Impaired BRCA2 binding to RAD51 / replication fork processing / Presynaptic phase of homologous DNA pairing and strand exchange / response to glucose / negative regulation of double-strand break repair via homologous recombination / interstrand cross-link repair / four-way junction DNA binding / Fanconi Anemia Pathway / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / PKR-mediated signaling / HDR through Homologous Recombination (HRR) / multicellular organism growth / glucose homeostasis / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / DNA replication / RNA helicase activity / nuclear speck / nuclear body / RNA helicase / DNA repair / nucleotide binding / chromatin binding / chromatin / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #510 / Helix Hairpins - #770 / RecQ-mediated genome instability protein 2 / RecQ-mediated genome instability protein 2 / Fanconi anemia group M protein, MHF binding domain / FANCM/Mph1-like / FANCM, DEAH-box helicase domain / : / FANCM to MHF binding domain / RecQ-mediated genome instability protein 1, C-terminal OB-fold domain ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #510 / Helix Hairpins - #770 / RecQ-mediated genome instability protein 2 / RecQ-mediated genome instability protein 2 / Fanconi anemia group M protein, MHF binding domain / FANCM/Mph1-like / FANCM, DEAH-box helicase domain / : / FANCM to MHF binding domain / RecQ-mediated genome instability protein 1, C-terminal OB-fold domain / RecQ-mediated genome instability protein 1, N-terminal helical domain superfamily / : / Recq-mediated genome instability protein 1, C-terminal OB-fold / RMI1, N-terminal helical domain / DUF1767 / RecQ mediated genome instability protein 1, N-terminal / RecQ mediated genome instability protein, N-terminal OB-fold superfamily / RMI1, N-terminal OB-fold domain / ERCC4 domain / ERCC4 domain / ERCC4 domain / RuvA domain 2-like / Restriction endonuclease type II-like / Helix Hairpins / Nucleic acid-binding proteins / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helix non-globular / Special / Helicase conserved C-terminal domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / 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 / Nucleic acid-binding, OB-fold / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Fanconi anemia group M protein / RecQ-mediated genome instability protein 2 / RecQ-mediated genome instability protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsHoadley, K.A. / Keck, J.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Defining the molecular interface that connects the Fanconi anemia protein FANCM to the Bloom syndrome dissolvasome.
Authors: Hoadley, K.A. / Xue, Y. / Ling, C. / Takata, M. / Wang, W. / Keck, J.L.
History
DepositionJan 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1May 16, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RecQ-mediated genome instability protein 1
B: RecQ-mediated genome instability protein 2
C: Fanconi anemia group M protein


Theoretical massNumber of molelcules
Total (without water)37,7693
Polymers37,7693
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-38 kcal/mol
Surface area13490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.312, 96.440, 99.025
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121

-
Components

#1: Protein RecQ-mediated genome instability protein 1 / BLM-associated protein of 75 kDa / BLAP75 / FAAP75


Mass: 17401.254 Da / Num. of mol.: 1 / Fragment: C-terminal OB domain (residues 473-625)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RMI1, C9orf76 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H9A7
#2: Protein RecQ-mediated genome instability protein 2 / hRMI2 / BLM-associated protein of 18 kDa / BLAP18


Mass: 16168.581 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RMI2, C16orf75 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96E14
#3: Protein/peptide Fanconi anemia group M protein / Protein FACM / ATP-dependent RNA helicase FANCM / Fanconi anemia-associated polypeptide of 250 kDa ...Protein FACM / ATP-dependent RNA helicase FANCM / Fanconi anemia-associated polypeptide of 250 kDa / FAAP250 / Protein Hef ortholog


Mass: 4199.458 Da / Num. of mol.: 1 / Fragment: MM2 peptide (residues 1218-1251)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FANCM, KIAA1596 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IYD8, RNA helicase

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 200 mM Na2SO4, 5% polyethylene glycol 3350, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 13, 2011
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. all: 5728 / Num. obs: 5711 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.081 / Χ2: 1.163 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.3-3.365.10.5872601.0291100
3.36-3.425.30.3822910.921199.7
3.42-3.485.20.382721.0671100
3.48-3.555.30.2782770.9651100
3.55-3.635.20.2652791.0471100
3.63-3.725.20.1862870.9571100
3.72-3.815.20.1732740.916199.6
3.81-3.915.10.1582881.0091100
3.91-4.035.20.1372921.0931100
4.03-4.165.20.1172871.182199.7
4.16-4.315.20.12681.3381100
4.31-4.485.10.0822871.4381100
4.48-4.6850.0792831.497199.6
4.68-4.935.20.0682941.4861100
4.93-5.245.10.0642801.2531100
5.24-5.6450.0652921.3121100
5.64-6.215.10.0522911.125199.7
6.21-7.150.0492931.1811100
7.1-8.944.90.0343001.24199.7
8.94-504.40.0263161.233196.9

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3mxn

3mxn


Resolution: 3.3→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.82 / WRfactor Rfree: 0.3042 / WRfactor Rwork: 0.1997 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7471 / SU B: 75.396 / SU ML: 0.557 / SU R Cruickshank DPI: 0.4697 / SU Rfree: 0.6787 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.679 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3254 273 4.8 %RANDOM
Rwork0.2165 ---
all0.2552 5728 --
obs0.2217 5711 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 100.78 Å2 / Biso mean: 92.948 Å2 / Biso min: 23.86 Å2
Baniso -1Baniso -2Baniso -3
1-5.44 Å20 Å20 Å2
2---0.05 Å20 Å2
3----5.38 Å2
Refinement stepCycle: LAST / Resolution: 3.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2098 0 0 0 2098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222135
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.9952885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8015265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.0422485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.33315394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2121515
X-RAY DIFFRACTIONr_chiral_restr0.0830.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211561
X-RAY DIFFRACTIONr_mcbond_it0.3751.51344
X-RAY DIFFRACTIONr_mcangle_it0.72922180
X-RAY DIFFRACTIONr_scbond_it0.9643791
X-RAY DIFFRACTIONr_scangle_it1.7484.5705
LS refinement shellResolution: 3.286→3.371 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 18 -
Rwork0.329 359 -
all-377 -
obs--97.16 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2813-0.89221.17333.2087-1.15254.8267-0.06310.241-0.33250.02730.02120.18270.2217-0.13360.04190.1566-0.01540.05430.0433-0.04450.068711.2933-6.81143.7276
25.8793-0.1754-1.21855.4824-1.78264.4032-0.0962-0.15630.39140.1208-0.01050.2627-0.2407-0.67750.10670.27770.1329-0.02010.1768-0.06810.06181.239910.66269.6541
39.9876-6.1070.398410.07340.46710.1701-0.218-0.6834-0.53220.7920.21110.52220.2195-0.21120.00690.80990.0802-0.02780.8229-0.02980.61227.0805-7.705220.0544
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A482 - 625
2X-RAY DIFFRACTION2B13 - 147
3X-RAY DIFFRACTION3C1226 - 1237

+
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