[English] 日本語
Yorodumi
- PDB-8gtx: Crystal Structure of human Spindlin1-HBx complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8gtx
TitleCrystal Structure of human Spindlin1-HBx complex
Components
  • HBx
  • Spindlin-1
KeywordsSTRUCTURAL PROTEIN / Tudor domain
Function / homology
Function and homology information


gamete generation / rRNA transcription / positive regulation of Wnt signaling pathway / methylated histone binding / meiotic cell cycle / Wnt signaling pathway / spindle / chromatin organization / nuclear membrane / regulation of DNA-templated transcription ...gamete generation / rRNA transcription / positive regulation of Wnt signaling pathway / methylated histone binding / meiotic cell cycle / Wnt signaling pathway / spindle / chromatin organization / nuclear membrane / regulation of DNA-templated transcription / nucleolus / positive regulation of DNA-templated transcription / nucleoplasm / nucleus / cytosol
Similarity search - Function
Spindlin/spermiogenesis-specific protein / Spindlin/spermiogenesis-specific domain superfamily / Spin/Ssty Family
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLi, H. / Liu, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)92153302 China
CitationJournal: To be published
Title: Crystal Structure of human Spindlin1-HBx complex
Authors: Liu, W. / Li, H.T.
History
DepositionSep 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Spindlin-1
B: HBx
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2504
Polymers27,0662
Non-polymers1842
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-14 kcal/mol
Surface area11880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.788, 67.096, 93.695
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Spindlin-1 / Ovarian cancer-related protein / Spindlin1


Mass: 24816.994 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPIN1, OCR, SPIN / Plasmid: pGex-6p / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y657
#2: Protein/peptide HBx


Mass: 2248.801 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.67 % / Mosaicity: 0.39 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 16%(w/v) PEG 8000, 0.04M Potassium phosphate dibasic, 20% (v/v) Glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 4, 2021 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 28755 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.043 / Rrim(I) all: 0.11 / Χ2: 0.836 / Net I/σ(I): 4.9 / Num. measured all: 185436
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.836.50.57714310.9050.2430.6270.531100
1.83-1.866.40.48513940.8980.2050.5280.60199.8
1.86-1.96.20.43113850.9170.1870.470.62299.7
1.9-1.946.10.35914170.9460.1580.3930.64799.9
1.94-1.986.80.32814430.9560.1350.3550.63399.9
1.98-2.036.80.28614090.9640.1190.310.73699.9
2.03-2.086.70.24414100.9660.1020.2650.809100
2.08-2.136.60.21414180.9750.090.2330.8599.9
2.13-2.26.50.19614170.9760.0830.2130.92199.9
2.2-2.276.30.1814280.9820.0780.1960.89599.9
2.27-2.355.90.15914280.9840.0710.1750.903100
2.35-2.446.80.15314250.9840.0630.1660.885100
2.44-2.556.80.13314340.9870.0550.1440.922100
2.55-2.696.60.11914480.9920.050.1290.92599.9
2.69-2.866.50.10314280.9920.0440.1120.89999.9
2.86-3.086.10.08714350.9920.0370.0951.02699.7
3.08-3.396.80.07614690.9950.0310.0821.05499.9
3.39-3.886.60.06414560.9960.0270.0691.06799.9
3.88-4.886.10.05314910.9970.0230.0580.99799.7
4.88-5060.04815890.9970.0210.0520.76299.7

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.17.1_3660refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4mzg

4mzg


Resolution: 1.8→46.85 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 17.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1967 1396 4.87 %
Rwork0.1631 27292 -
obs0.1647 28688 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.53 Å2 / Biso mean: 23.835 Å2 / Biso min: 9.23 Å2
Refinement stepCycle: final / Resolution: 1.8→46.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1765 0 12 302 2079
Biso mean--34.64 33.62 -
Num. residues----220
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.860.26061400.20672599273996
1.86-1.930.25651350.185426742809100
1.93-2.020.22741260.172227132839100
2.02-2.130.17561350.158527112846100
2.13-2.260.17471360.154427122848100
2.26-2.440.21891450.171827172862100
2.44-2.680.21921520.170227402892100
2.68-3.070.20441250.170227482873100
3.07-3.870.17931480.151527742922100
3.87-46.850.17441540.15392904305899

+
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://pdbjlvh1.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