[English] 日本語
Yorodumi
- PDB-6r3p: Crystal structure of human DMC1 ATPase domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6r3p
TitleCrystal structure of human DMC1 ATPase domain
ComponentsMeiotic recombination protein DMC1/LIM15 homologGenetic recombination
KeywordsRECOMBINATION / Recombinase / Homologous recombination / Strand invasion / Meiosis
Function / homology
Function and homology information


female gamete generation / chromosome organization involved in meiotic cell cycle / DNA recombinase assembly / homologous chromosome pairing at meiosis / double-strand break repair involved in meiotic recombination / mitotic recombination / DNA strand invasion / DNA strand exchange activity / lateral element / oocyte maturation ...female gamete generation / chromosome organization involved in meiotic cell cycle / DNA recombinase assembly / homologous chromosome pairing at meiosis / double-strand break repair involved in meiotic recombination / mitotic recombination / DNA strand invasion / DNA strand exchange activity / lateral element / oocyte maturation / reciprocal meiotic recombination / ATP-dependent DNA damage sensor activity / male meiosis I / spermatid development / ATP-dependent activity, acting on DNA / ovarian follicle development / meiotic cell cycle / condensed nuclear chromosome / Meiotic recombination / single-stranded DNA binding / site of double-strand break / chromosome / double-stranded DNA binding / spermatogenesis / chromosome, telomeric region / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / nucleus
Similarity search - Function
Meiotic recombination protein Dmc1 / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain ...Meiotic recombination protein Dmc1 / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Meiotic recombination protein DMC1/LIM15 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsDunce, J.M. / Davies, O.R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust104158/Z/14/Z United Kingdom
Royal SocietyRG170118 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of human DMC1 ATPase domain
Authors: Dunce, J.M. / Davies, O.R.
History
DepositionMar 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Meiotic recombination protein DMC1/LIM15 homolog
B: Meiotic recombination protein DMC1/LIM15 homolog
C: Meiotic recombination protein DMC1/LIM15 homolog
D: Meiotic recombination protein DMC1/LIM15 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,80912
Polymers115,4754
Non-polymers1,3348
Water5,278293
1
A: Meiotic recombination protein DMC1/LIM15 homolog
B: Meiotic recombination protein DMC1/LIM15 homolog
hetero molecules

A: Meiotic recombination protein DMC1/LIM15 homolog
B: Meiotic recombination protein DMC1/LIM15 homolog
hetero molecules

A: Meiotic recombination protein DMC1/LIM15 homolog
B: Meiotic recombination protein DMC1/LIM15 homolog
hetero molecules

A: Meiotic recombination protein DMC1/LIM15 homolog
B: Meiotic recombination protein DMC1/LIM15 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,44716
Polymers230,9508
Non-polymers4978
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation3_555-y,x,z1
2
C: Meiotic recombination protein DMC1/LIM15 homolog
D: Meiotic recombination protein DMC1/LIM15 homolog
hetero molecules

C: Meiotic recombination protein DMC1/LIM15 homolog
D: Meiotic recombination protein DMC1/LIM15 homolog
hetero molecules

C: Meiotic recombination protein DMC1/LIM15 homolog
D: Meiotic recombination protein DMC1/LIM15 homolog
hetero molecules

C: Meiotic recombination protein DMC1/LIM15 homolog
D: Meiotic recombination protein DMC1/LIM15 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,78832
Polymers230,9508
Non-polymers4,83824
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation3_655-y+1,x,z1
Unit cell
Length a, b, c (Å)174.490, 174.490, 179.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Meiotic recombination protein DMC1/LIM15 homolog / Genetic recombination


Mass: 28868.811 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DMC1, DMC1H, LIM15 / Plasmid: pHAT4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q14565

-
Non-polymers , 6 types, 301 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.96 Å3/Da / Density % sol: 58.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 50 mM HEPES-NaOH pH 7.2, 50 mM MgCl2, 500 mM NaCl, 7.5 % PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.05→47.49 Å / Num. obs: 86315 / % possible obs: 100 % / Redundancy: 15 % / Biso Wilson estimate: 58.74 Å2 / CC1/2: 1 / Rpim(I) all: 0.034 / Rrim(I) all: 0.096 / Net I/σ(I): 19.5
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 15.5 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4545 / CC1/2: 0.628 / Rpim(I) all: 0.72 / Rrim(I) all: 2.038 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HYY

4hyy


Resolution: 2.05→47.011 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0.33 / Phase error: 23.57
RfactorNum. reflection% reflectionSelection details
Rfree0.2191 8011 4.82 %Random selection
Rwork0.1942 ---
obs0.1954 86291 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.05→47.011 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7704 0 89 293 8086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027958
X-RAY DIFFRACTIONf_angle_d0.47810673
X-RAY DIFFRACTIONf_dihedral_angle_d14.1182981
X-RAY DIFFRACTIONf_chiral_restr0.0421169
X-RAY DIFFRACTIONf_plane_restr0.0031385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.07330.34492080.31335362X-RAY DIFFRACTION100
2.0733-2.09770.32082640.29975258X-RAY DIFFRACTION100
2.0977-2.12330.29962520.29445295X-RAY DIFFRACTION100
2.1233-2.15020.29532750.29985290X-RAY DIFFRACTION100
2.1502-2.17850.32092430.27025347X-RAY DIFFRACTION100
2.1785-2.20830.26642390.25985193X-RAY DIFFRACTION100
2.2083-2.23980.29272820.24945286X-RAY DIFFRACTION100
2.2398-2.27330.29192550.25345268X-RAY DIFFRACTION100
2.2733-2.30880.27792730.24745279X-RAY DIFFRACTION100
2.3088-2.34670.26193020.24345229X-RAY DIFFRACTION100
2.3467-2.38710.25652930.23435264X-RAY DIFFRACTION100
2.3871-2.43050.24523190.21935202X-RAY DIFFRACTION100
2.4305-2.47730.23742540.225273X-RAY DIFFRACTION100
2.4773-2.52780.24822560.22355274X-RAY DIFFRACTION100
2.5278-2.58280.23942680.22485272X-RAY DIFFRACTION100
2.5828-2.64290.23953240.21095235X-RAY DIFFRACTION100
2.6429-2.7090.23362890.20585208X-RAY DIFFRACTION100
2.709-2.78220.23222640.22185316X-RAY DIFFRACTION100
2.7822-2.8640.2482460.21765291X-RAY DIFFRACTION100
2.864-2.95650.23532490.22865268X-RAY DIFFRACTION100
2.9565-3.06210.23863030.21925268X-RAY DIFFRACTION100
3.0621-3.18470.22962380.20265262X-RAY DIFFRACTION100
3.1847-3.32960.23572540.19665312X-RAY DIFFRACTION100
3.3296-3.50510.20262640.17625244X-RAY DIFFRACTION100
3.5051-3.72460.18332780.16835298X-RAY DIFFRACTION100
3.7246-4.01210.17642540.15715300X-RAY DIFFRACTION100
4.0121-4.41550.16922890.13825215X-RAY DIFFRACTION100
4.4155-5.05380.16631980.14475358X-RAY DIFFRACTION100
5.0538-6.36480.23453080.17725241X-RAY DIFFRACTION100
6.3648-47.02290.20922700.20285250X-RAY DIFFRACTION99
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)
12.9201-0.58010.53875.33720.08971.10060.0269-0.0762-0.21460.0431-0.02440.20570.0916-0.08130.02240.394-0.0371-0.03960.3844-0.04410.324334.604523.880271.4306
25.22420.38561.89396.96371.08248.813-0.11140.8754-0.2525-1.29440.28530.3462-0.0931-0.7247-0.21390.86030.0174-0.0480.588-0.00750.349736.013424.941351.4052
36.8828-0.49780.12392.74810.5371.062-0.11530.13780.0340.07050.1088-0.02920.01590.01290.0250.3607-0.0126-0.01470.4045-0.05220.29837.749241.344971.3158
45.26340.92534.25588.09983.63927.61580.34171.1265-0.0853-0.80920.0344-0.20950.335-0.5034-0.37190.6604-0.0546-0.02631.12420.06880.43927.750643.223951.5042
54.6907-0.33770.24662.1991-0.58741.30370.03040.35470.1152-0.1201-0.02410.06320.0709-0.0262-0.00130.3278-0.02160.00840.30360.00550.254483.174945.630170.866
62.0041-0.8985-3.36968.6364-2.77528.05020.46570.68960.2854-1.1168-0.15480.1097-0.27890.7429-0.29330.67880.0265-0.02461.1333-0.06990.3983.137144.260651.2499
73.0457-0.8847-0.0873.7249-0.33641.2690.08510.13760.206-0.1088-0.0843-0.1857-0.04310.00220.0080.2883-0.04550.0150.32140.00880.258354.810560.714771.0282
85.82880.4216-1.39296.62471.02138.53680.07271.234-0.0016-1.00350.1719-0.35290.22370.7329-0.21840.74970.05320.00080.7151-0.01480.301853.363559.446351.0212
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 82:300)
2X-RAY DIFFRACTION2(chain A and resid 301:340)
3X-RAY DIFFRACTION3(chain B and resid 83:300)
4X-RAY DIFFRACTION4(chain B and resid 301:340)
5X-RAY DIFFRACTION5(chain C and resid 81:301)
6X-RAY DIFFRACTION6(chain C and resid 302:338)
7X-RAY DIFFRACTION7(chain D and resid 82:300)
8X-RAY DIFFRACTION8(chain D and resid 301:340)

+
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