[English] 日本語
Yorodumi
- PDB-6f5x: Crystal structure of the SYCP1 N-terminal head-to-head assembly i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6f5x
TitleCrystal structure of the SYCP1 N-terminal head-to-head assembly in closed conformation
ComponentsSynaptonemal complex protein 1
KeywordsSTRUCTURAL PROTEIN / Meiosis / Chromosome structure / Coiled-coil / Self-assembly
Function / homology
Function and homology information


transverse filament / lateral element assembly / meiotic DNA repair synthesis / chiasma assembly / autosome / central element / sperm DNA condensation / synaptonemal complex assembly / homologous chromosome pairing at meiosis / synaptonemal complex ...transverse filament / lateral element assembly / meiotic DNA repair synthesis / chiasma assembly / autosome / central element / sperm DNA condensation / synaptonemal complex assembly / homologous chromosome pairing at meiosis / synaptonemal complex / reciprocal meiotic recombination / chromosome, centromeric region / Meiotic synapsis / male germ cell nucleus / regulation of protein localization / chromosome / spermatogenesis / double-stranded DNA binding / protein homotetramerization / cell division / DNA binding
Similarity search - Function
Synaptonemal complex protein 1 / Synaptonemal complex protein 1 (SCP-1)
Similarity search - Domain/homology
IODIDE ION / TRIETHYLENE GLYCOL / Synaptonemal complex protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.91 Å
AuthorsRatcliff, M. / Dunce, J.M. / Davies, O.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust and Royal Society104158/Z/14/Z United Kingdom
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Structural basis of meiotic chromosome synapsis through SYCP1 self-assembly.
Authors: Dunce, J.M. / Dunne, O.M. / Ratcliff, M. / Millan, C. / Madgwick, S. / Uson, I. / Davies, O.R.
History
DepositionDec 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 1, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Synaptonemal complex protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5734
Polymers9,1691
Non-polymers4043
Water57632
1
A: Synaptonemal complex protein 1
hetero molecules

A: Synaptonemal complex protein 1
hetero molecules

A: Synaptonemal complex protein 1
hetero molecules

A: Synaptonemal complex protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,29016
Polymers36,6744
Non-polymers1,61612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area9600 Å2
ΔGint-73 kcal/mol
Surface area24010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.640, 39.380, 165.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-324-

HOH

21A-331-

HOH

-
Components

#1: Protein Synaptonemal complex protein 1 / / SCP-1 / Cancer/testis antigen 8 / CT8


Mass: 9168.571 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYCP1, SCP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15431
#2: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.55 Å3/Da / Density % sol: 51.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 140 mM NaCl, 70 mM Na/K phosphate pH 6.2, 35% (v/v) PEG200; soaked in 40% (v/v) PEG200 and 100 mM NaI

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.7712 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 1.91→41.44 Å / Num. obs: 7678 / % possible obs: 99.3 % / Redundancy: 5.9 % / Biso Wilson estimate: 33.34 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.028 / Rpim(I) all: 0.017 / Rrim(I) all: 0.036 / Net I/σ(I): 27.9
Reflection shellResolution: 1.91→1.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.678 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 464 / CC1/2: 0.839 / Rpim(I) all: 0.541 / Rrim(I) all: 0.873 / % possible all: 92.1

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.91→41.44 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 25.34
Details: Refined against data corrected for anisotropy (FP_ISOB/SIGFP_ISOB) using the UCLA diffraction anisotropy server.
RfactorNum. reflection% reflection
Rfree0.2392 324 4.8 %
Rwork0.2272 --
obs0.2278 6754 87.97 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 58.4 Å2
Refinement stepCycle: LAST / Resolution: 1.91→41.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms624 0 12 32 668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009648
X-RAY DIFFRACTIONf_angle_d1.022857
X-RAY DIFFRACTIONf_dihedral_angle_d10.579273
X-RAY DIFFRACTIONf_chiral_restr0.05392
X-RAY DIFFRACTIONf_plane_restr0.004108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9118-2.03160.3309280.3174437X-RAY DIFFRACTION38
2.0316-2.18840.2647610.27531078X-RAY DIFFRACTION91
2.1884-2.40860.2572560.22781188X-RAY DIFFRACTION100
2.4086-2.75710.225520.26131206X-RAY DIFFRACTION100
2.7571-3.47340.264640.24761232X-RAY DIFFRACTION100
3.4734-41.45220.2158630.19451289X-RAY DIFFRACTION98

+
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