[English] 日本語
Yorodumi
- PDB-4hs2: Crystal Structure of the Human SPOP C-terminal Domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hs2
TitleCrystal Structure of the Human SPOP C-terminal Domain
ComponentsSpeckle-type POZ protein
KeywordsPROTEIN BINDING / protein interaction domain / Oligomerisation
Function / homology
Function and homology information


regulation of proteolysis / Cul3-RING ubiquitin ligase complex / molecular function inhibitor activity / Hedgehog 'on' state / protein polyubiquitination / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear speck / ubiquitin protein ligase binding / nucleoplasm / identical protein binding ...regulation of proteolysis / Cul3-RING ubiquitin ligase complex / molecular function inhibitor activity / Hedgehog 'on' state / protein polyubiquitination / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear speck / ubiquitin protein ligase binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #420 / SPOP, C-terminal BACK domain / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #420 / SPOP, C-terminal BACK domain / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Speckle-type POZ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.53 Å
AuthorsVan Geersdaele, L.K. / Stead, M.A. / Carr, S.B. / Wright, S.C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural basis of high-order oligomerization of the cullin-3 adaptor SPOP.
Authors: van Geersdaele, L.K. / Stead, M.A. / Harrison, C.M. / Carr, S.B. / Close, H.J. / Rosbrook, G.O. / Connell, S.D. / Wright, S.C.
History
DepositionOct 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Speckle-type POZ protein


Theoretical massNumber of molelcules
Total (without water)11,9411
Polymers11,9411
Non-polymers00
Water1,11762
1
A: Speckle-type POZ protein

A: Speckle-type POZ protein


Theoretical massNumber of molelcules
Total (without water)23,8832
Polymers23,8832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area1370 Å2
ΔGint-13 kcal/mol
Surface area7010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.650, 57.650, 102.810
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-411-

HOH

-
Components

#1: Protein Speckle-type POZ protein / HIB homolog 1 / Roadkill homolog 1


Mass: 11941.446 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 270-374) / Mutation: L273D, L282D, L285K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPOP / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS; B834 / References: UniProt: O43791
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.07 Å3/Da / Density % sol: 40.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 26% PEG 1500, 7% isopropanol, 0.1M CaCl2, 0.1M imidazole pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I04-110.9173
SYNCHROTRONDiamond I0220.9795
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2011
Radiation
IDProtocolScattering typeWavelength-ID
1SINGLE WAVELENGTHx-ray1
2SINGLE WAVELENGTHx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.91731
20.97951
ReflectionRedundancy: 71.5 % / Av σ(I) over netI: 3.4 / Number: 442290 / Rsym value: 0.185 / D res high: 2.125 Å / D res low: 51.405 Å / Num. obs: 6183 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
9.551.499.810.0310.03153.4
6.729.510010.0420.04258.6
5.496.7210010.0820.08265.8
4.755.4910010.0760.07670.9
4.254.7510010.0680.06874.9
3.884.2510010.0810.08164.8
3.593.8810010.1010.10169.4
3.363.5999.610.1220.12272.8
3.173.3610010.1720.17274.7
33.1710010.1920.19275.6
2.86310010.2490.24977.8
2.742.8610010.2620.26272.7
2.642.7410010.3270.32768.7
2.542.6410010.3630.36373.5
2.452.5410010.4420.44276
2.382.4599.710.4570.45776.2
2.32.3810010.5570.55775.7
2.242.310010.6440.64474.7
2.182.2410010.8850.88571.9
2.122.1810010.8990.89960.1
ReflectionResolution: 1.528→51.405 Å / Num. all: 16004 / Num. obs: 16004 / % possible obs: 99.8 % / Redundancy: 11.6 % / Rsym value: 0.056 / Net I/σ(I): 24.2
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.53-1.578.30.6471.2954011430.64799.9
1.57-1.6110.80.5251.51230011400.52599.9
1.61-1.6612.30.4111.91334910810.41199.9
1.66-1.7112.30.3352.31312910670.33599.9
1.71-1.7612.30.253.11246010170.2599.8
1.76-1.8312.30.2013.9122299980.20199.8
1.83-1.912.40.1684.7120269730.168100
1.9-1.9712.20.1196.4114629410.11999.9
1.97-2.0612.20.0898.7111439150.089100
2.06-2.1612.30.06811104188460.068100
2.16-2.2812.20.05812.6101888360.058100
2.28-2.4212.20.04914.795997880.049100
2.42-2.5812.10.04714.388267270.04799.6
2.58-2.7911.90.04114.683157010.041100
2.79-3.0611.30.03916.373476530.039100
3.06-3.4211.20.03716.566205920.037100
3.42-3.9411.40.03616.460375310.03699.8
3.94-4.83110.03118.751274650.031100
4.83-6.8310.90.0321940203690.032100
6.83-51.4058.60.02822.318942210.02891.5

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
XDSdata reduction
SCALAdata scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.53→27.75 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.975 / WRfactor Rfree: 0.1444 / WRfactor Rwork: 0.1267 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9316 / SU B: 1.61 / SU ML: 0.027 / SU R Cruickshank DPI: 0.0512 / SU Rfree: 0.0469 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.051 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1512 794 5 %RANDOM
Rwork0.132 ---
obs0.1329 15153 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.41 Å2 / Biso mean: 21.2669 Å2 / Biso min: 11.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.05 Å20 Å2
2---0.1 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.53→27.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms489 0 0 62 551
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.019558
X-RAY DIFFRACTIONr_bond_other_d0.0010.02337
X-RAY DIFFRACTIONr_angle_refined_deg1.1691.932771
X-RAY DIFFRACTIONr_angle_other_deg0.9573842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.196577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.9252625
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.9671590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.714151
X-RAY DIFFRACTIONr_chiral_restr0.0720.290
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02666
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02107
X-RAY DIFFRACTIONr_rigid_bond_restr6.3733894
X-RAY DIFFRACTIONr_sphericity_free30.104525
X-RAY DIFFRACTIONr_sphericity_bonded14.2815916
LS refinement shellResolution: 1.528→1.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 52 -
Rwork0.218 944 -
all-996 -
obs--99.9 %

+
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