[English] 日本語
Yorodumi
- PDB-6bzg: Structure of S. cerevisiae Zip2:Spo16 complex, P212121 form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bzg
TitleStructure of S. cerevisiae Zip2:Spo16 complex, P212121 form
Components
  • Protein ZIP2
  • Sporulation-specific protein 16
KeywordsDNA BINDING PROTEIN / XPF-ERCC1 / Meiosis / Recombination
Function / homology
Function and homology information


regulation of synaptonemal complex assembly / synapsis initiation complex / regulation of reciprocal meiotic recombination / DNA secondary structure binding / ascospore formation / synaptonemal complex assembly / homologous chromosome pairing at meiosis / synaptonemal complex / positive regulation of protein sumoylation / homologous recombination ...regulation of synaptonemal complex assembly / synapsis initiation complex / regulation of reciprocal meiotic recombination / DNA secondary structure binding / ascospore formation / synaptonemal complex assembly / homologous chromosome pairing at meiosis / synaptonemal complex / positive regulation of protein sumoylation / homologous recombination / reciprocal meiotic recombination / protein sumoylation / condensed nuclear chromosome / nucleotide binding / mitochondrion
Similarity search - Function
Spo16 protein / Spo16 protein, N-terminal
Similarity search - Domain/homology
Sporulation-specific protein 16 / Protein ZIP2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.13 Å
AuthorsArora, K. / Corbett, K.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM104141 United States
Citation
Journal: Nucleic Acids Res. / Year: 2019
Title: The conserved XPF:ERCC1-like Zip2:Spo16 complex controls meiotic crossover formation through structure-specific DNA binding.
Authors: Arora, K. / Corbett, K.D.
#1: Journal: Biorxiv / Year: 2018
Title: Structure of Zip2:Spo16, a conserved XPF:ERCC1-like complex critical for meiotic crossover formation
Authors: Arora, K. / Corbett, K.D.
History
DepositionDec 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.2Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Revision 1.3Mar 27, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Protein ZIP2
A: Sporulation-specific protein 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8435
Polymers47,3682
Non-polymers4743
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-57 kcal/mol
Surface area19590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.249, 96.212, 101.445
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Protein ZIP2 / Zipping up meiotic chromosomes protein 2


Mass: 24345.135 Da / Num. of mol.: 1 / Mutation: K641A, E642A, K643A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ZIP2 / Production host: Escherichia coli (E. coli) / References: UniProt: P53061
#2: Protein Sporulation-specific protein 16


Mass: 23023.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SPO16 / Production host: Escherichia coli (E. coli) / References: UniProt: P17122
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.59 Å3/Da / Density % sol: 52.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM Bis Tris pH 5.5, 200 mM Ammonium sulfate, 15% PEG-3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.13→100 Å / Num. obs: 28219 / % possible obs: 99.8 % / Redundancy: 6.3 % / CC1/2: 0.987 / Rsym value: 0.207 / Net I/σ(I): 5.2
Reflection shellResolution: 2.13→2.19 Å / Num. unique obs: 15501 / CC1/2: 0.484 / Rsym value: 2.074

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
SHELXphasing
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.13→69.809 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.2 / Phase error: 32.61
RfactorNum. reflection% reflection
Rfree0.2704 2710 5.18 %
Rwork0.2492 --
obs0.2503 52319 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.13→69.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3219 0 29 74 3322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023306
X-RAY DIFFRACTIONf_angle_d0.3944458
X-RAY DIFFRACTIONf_dihedral_angle_d12.1241976
X-RAY DIFFRACTIONf_chiral_restr0.039505
X-RAY DIFFRACTIONf_plane_restr0.002559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.16880.41951330.37112541X-RAY DIFFRACTION95
2.1688-2.21050.40241750.3632588X-RAY DIFFRACTION98
2.2105-2.25560.36211670.35012599X-RAY DIFFRACTION99
2.2556-2.30470.35631290.34122655X-RAY DIFFRACTION100
2.3047-2.35830.36751350.33662676X-RAY DIFFRACTION100
2.3583-2.41730.34951240.32962622X-RAY DIFFRACTION100
2.4173-2.48260.36981340.31722628X-RAY DIFFRACTION99
2.4826-2.55570.30681510.31962637X-RAY DIFFRACTION99
2.5557-2.63820.36581420.30542650X-RAY DIFFRACTION99
2.6382-2.73250.35061600.30672588X-RAY DIFFRACTION99
2.7325-2.84190.36941600.31232638X-RAY DIFFRACTION99
2.8419-2.97120.28681210.29332647X-RAY DIFFRACTION99
2.9712-3.12790.33761250.26842590X-RAY DIFFRACTION98
3.1279-3.32380.31321160.26912621X-RAY DIFFRACTION97
3.3238-3.58040.22361860.24192549X-RAY DIFFRACTION98
3.5804-3.94070.29021310.22352586X-RAY DIFFRACTION98
3.9407-4.51090.22221410.19412604X-RAY DIFFRACTION97
4.5109-5.68280.20861390.20432563X-RAY DIFFRACTION97
5.6828-69.84630.20191410.21372627X-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)
12.8044-0.28870.58964.54360.96693.19840.02490.1405-0.4493-0.07580.1049-0.78570.17310.4676-0.1020.3499-0.04520.09130.6772-0.11970.762538.086133.80767.3148
26.42560.2328-3.85072.8117-1.75198.5141-0.0077-0.02110.3080.05190.21540.27840.1588-0.5594-0.29040.62-0.11610.0320.4247-0.09630.3383-0.652837.0641104.4365
33.1978-0.4465-2.44311.1257-0.02736.835-0.0868-0.1777-0.25710.0629-0.16790.26640.4445-0.08770.27560.3955-0.02740.08170.2390.02380.41269.003832.814693.6759
43.86511.2721-0.30974.86971.01423.7229-0.04750.405-0.1807-0.08810.01510.2311-0.1534-0.42950.05230.29410.0890.02020.4139-0.04280.320118.206740.362370.1367
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 144 )
2X-RAY DIFFRACTION2chain 'A' and (resid 151 through 197 )
3X-RAY DIFFRACTION3chain 'B' and (resid 646 through 704 )
4X-RAY DIFFRACTION4chain 'B' and (resid 499 through 635 )

+
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