[English] 日本語
Yorodumi
- PDB-4yv4: Structure of the C. elegans SAS-5 coiled coil domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yv4
TitleStructure of the C. elegans SAS-5 coiled coil domain
ComponentsSpindle assembly abnormal protein 5
KeywordsSTRUCTURAL PROTEIN / coiled coil / trimer / a-helical / cell cycle
Function / homologycentriole assembly / centriole replication / centrosome duplication / centriole / cytoplasm / PHOSPHATE ION / Spindle assembly abnormal protein 5
Function and homology information
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsRogala, K.B. / Hatzopoulos, G.N. / Vakonakis, I.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J008265/1 United Kingdom
Wellcome Trust088497/Z/09/Z United Kingdom
CitationJournal: Elife / Year: 2015
Title: The Caenorhabditis elegans protein SAS-5 forms large oligomeric assemblies critical for centriole formation.
Authors: Rogala, K.B. / Dynes, N.J. / Hatzopoulos, G.N. / Yan, J. / Pong, S.K. / Robinson, C.V. / Deane, C.M. / Gonczy, P. / Vakonakis, I.
History
DepositionMar 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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: Spindle assembly abnormal protein 5
B: Spindle assembly abnormal protein 5
C: Spindle assembly abnormal protein 5
D: Spindle assembly abnormal protein 5
E: Spindle assembly abnormal protein 5
F: Spindle assembly abnormal protein 5
G: Spindle assembly abnormal protein 5
H: Spindle assembly abnormal protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,48313
Polymers55,0058
Non-polymers4785
Water4,486249
1
A: Spindle assembly abnormal protein 5


Theoretical massNumber of molelcules
Total (without water)6,8761
Polymers6,8761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4870 Å2
MethodPISA
2
B: Spindle assembly abnormal protein 5
C: Spindle assembly abnormal protein 5
D: Spindle assembly abnormal protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8185
Polymers20,6273
Non-polymers1912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-59 kcal/mol
Surface area12280 Å2
MethodPISA
3
E: Spindle assembly abnormal protein 5
G: Spindle assembly abnormal protein 5
H: Spindle assembly abnormal protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9146
Polymers20,6273
Non-polymers2873
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-76 kcal/mol
Surface area12600 Å2
MethodPISA
4
F: Spindle assembly abnormal protein 5


Theoretical massNumber of molelcules
Total (without water)6,8761
Polymers6,8761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.600, 55.070, 191.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThere are two copies of the biologically relevant assembly in the asymmetric unit, comprising chains B,C and D (copy 1) and E, G, and H (copy 2). The correct oligomerization size and orientation of chains was determined experimentally in solution. Chains A and F correspond to crystallographic packing artefacts.

-
Components

#1: Protein
Spindle assembly abnormal protein 5


Mass: 6875.661 Da / Num. of mol.: 8 / Fragment: UNP residues 125-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: sas-5, F35B12.5 / Plasmid: pFLOAT / Details (production host): pET30a derivative / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q20010
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MOPS/HEPES-Na pH 7.5, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% w/v MPD, 0.03 M NaNO3, 0.03 M Na2HPO4, 0.03 M (NH4)2SO4
PH range: 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→32.1 Å / Num. obs: 31718 / % possible obs: 68.2 % / Redundancy: 2 % / Biso Wilson estimate: 32.35 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 11.3
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 0.1 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 3.9 / % possible all: 3.9

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→32.1 Å / Cor.coef. Fo:Fc: 0.9408 / Cor.coef. Fo:Fc free: 0.9244 / SU R Cruickshank DPI: 0.213 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.227 / SU Rfree Blow DPI: 0.175 / SU Rfree Cruickshank DPI: 0.172
RfactorNum. reflection% reflectionSelection details
Rfree0.2392 1600 5.04 %RANDOM
Rwork0.2108 ---
obs0.2123 31718 67.84 %-
Displacement parametersBiso mean: 51.24 Å2
Baniso -1Baniso -2Baniso -3
1--6.2821 Å20 Å20 Å2
2--1.2079 Å20 Å2
3---5.0742 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 1.8→32.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3647 0 25 249 3921
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013708HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.964984HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1455SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes170HARMONIC2
X-RAY DIFFRACTIONt_gen_planes496HARMONIC5
X-RAY DIFFRACTIONt_it3708HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.2
X-RAY DIFFRACTIONt_other_torsion18.8
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion497SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4521SEMIHARMONIC4
LS refinement shellResolution: 1.8→1.86 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.3087 12 6.49 %
Rwork0.2103 173 -
all0.2153 185 -
obs--4.35 %
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)
13.19490.2261.36922.0987-1.81039.9416-0.15450.3458-0.3282-0.0210.0347-0.10930.27020.11020.1197-0.2420.04970.0028-0.1009-0.0807-0.099714.294621.28143.9163
22.44010.70662.00892.49720.8659.6432-0.0183-0.0074-0.10790.2448-0.0021-0.12640.35610.12920.0204-0.35110.0046-0.0027-0.2576-0.0458-0.223219.126826.84157.8562
30.1287-0.1509-0.73220.78991.962611.969-0.0239-0.05-0.07280.02750.0540.0283-0.00790.2437-0.0301-0.40140.0302-0.0164-0.148-0.0637-0.206929.192531.539759.434
41.0905-0.0421-0.32650.68641.475314.04070.09450.02850.0654-0.02780.0862-0.0274-0.6281-0.1857-0.1807-0.35920.0319-0.0071-0.2955-0.0474-0.229118.940935.138163.4761
52.4263-0.1042-2.15483.55690.30966.1472-0.006-0.11350.0701-0.40310.1027-0.1899-0.61830.2015-0.0967-0.4281-0.04020.0046-0.1911-0.0893-0.220442.69125.898630.2486
62.3804-0.307-0.30851.6323-0.28249.352-0.1514-0.07760.36970.0162-0.0554-0.0665-0.59220.69060.2068-0.1335-0.0370.0163-0.0472-0.0082-0.083637.675930.101245.4554
70.691-0.2978-0.88520.41640.26349.36250.09170.0083-0.0178-0.03230.11140.03840.2625-0.0715-0.2031-0.2763-0.0494-0.0009-0.2144-0.0421-0.191541.951618.584524.0675
80.10430.02622.05330.64632.101412.6869-0.0264-0.08990.0961-0.0057-0.01780.03830.10180.22530.0442-0.315-0.04060.0101-0.0262-0.0799-0.196752.332321.098227.8978
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|129 - A|175 }
2X-RAY DIFFRACTION2{ B|129 - B|179 }
3X-RAY DIFFRACTION3{ C|123 - C|179 }
4X-RAY DIFFRACTION4{ D|124 - D|179 }
5X-RAY DIFFRACTION5{ E|127 - E|179 }
6X-RAY DIFFRACTION6{ F|127 - F|176 }
7X-RAY DIFFRACTION7{ G|124 - G|179 }
8X-RAY DIFFRACTION8{ H|123 - H|179 }

+
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://pdbjlc1.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