[English] 日本語
Yorodumi
- PDB-3d9h: Crystal Structure of the Splice Variant of Human ASB9 (hASB9-2), ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3d9h
TitleCrystal Structure of the Splice Variant of Human ASB9 (hASB9-2), an Ankyrin Repeat Protein
ComponentscDNA FLJ77766, highly similar to Homo sapiens ankyrin repeat and SOCS box-containing 9 (ASB9), transcript variant 2, mRNA
KeywordsSTRUCTURAL PROTEIN / PROTEIN BINDING / ASB9 / ANK repeat / L-shaped / alpha-helices
Function / homology
Function and homology information


post-translational protein modification / positive regulation of protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / protein ubiquitination / intracellular signal transduction / mitochondrion / cytosol
Similarity search - Function
Ankyrin repeat and SOCS box protein 9/11, SOCS box domain / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / Domain of unknown function DUF3447 / Ankyrin repeat-containing domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. ...Ankyrin repeat and SOCS box protein 9/11, SOCS box domain / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / Domain of unknown function DUF3447 / Ankyrin repeat-containing domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Ankyrin repeat and SOCS box protein 9 / Ankyrin repeat and SOCS box protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsFei, X. / Gu, X. / Fan, S. / Zhang, C. / Ji, C.
CitationJournal: To be published
Title: Crystal Structure of the Splice Variant of Human ASB9 (hASB9-2), an Ankyrin Repeat Protein
Authors: Fei, X. / Gu, X. / Fan, S. / Zhang, Y. / Li, F. / Zhang, C. / Gong, W. / Mao, Y. / Ji, C.
History
DepositionMay 27, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: cDNA FLJ77766, highly similar to Homo sapiens ankyrin repeat and SOCS box-containing 9 (ASB9), transcript variant 2, mRNA


Theoretical massNumber of molelcules
Total (without water)30,4251
Polymers30,4251
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.254, 129.254, 129.254
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-23-

ARG

DetailsTHERE ARE SOME CLOSE CONTACTS BASED ON CRYSTAL SYMMETRY IN THIS ENTRY. THEREFORE, PISA CAN NOT SUGGEST ANY POSSIBLE QUATERNARY STRUCTURE. PLEASE SEE THE DETAILS IN REMARK 3.

-
Components

#1: Protein cDNA FLJ77766, highly similar to Homo sapiens ankyrin repeat and SOCS box-containing 9 (ASB9), transcript variant 2, mRNA / Ankyrin repeat and SOCS box-containing 9 / isoform CRA_b / hASB9-2


Mass: 30425.484 Da / Num. of mol.: 1 / Mutation: A207V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: hASB9-2 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta / References: UniProt: A8K8A5, UniProt: Q96DX5*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.96 Å3/Da / Density % sol: 58.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Imidazole pH 6.5, 1.0M Sodium acetate trihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 22, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 19383 / Num. obs: 19367 / % possible obs: 100 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 44.3 / Num. measured all: 709934
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 6.5 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N11

1n11


Resolution: 2.2→35.85 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.253 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; The segments from Phe19 to Ser26 in two crystallographic symmetry-related molecules are related by a crystallographic 2-fold axis, and ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; The segments from Phe19 to Ser26 in two crystallographic symmetry-related molecules are related by a crystallographic 2-fold axis, and their densities overlap. So the depositors had to ignore the close contacts between these two segments given by validation software and assigned the occupancy of each segment to 0.5 to avoid clash.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 996 5.2 %RANDOM
Rwork0.194 ---
obs0.196 18322 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.468 Å2
Refinement stepCycle: LAST / Resolution: 2.2→35.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1823 0 0 157 1980
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211874
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.9462565
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6125249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60224.64384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43315304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2611510
X-RAY DIFFRACTIONr_chiral_restr0.0980.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021444
X-RAY DIFFRACTIONr_nbd_refined0.220.2895
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21240
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2145
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1030.216
X-RAY DIFFRACTIONr_mcbond_it0.931.51232
X-RAY DIFFRACTIONr_mcangle_it1.55621920
X-RAY DIFFRACTIONr_scbond_it2.4393719
X-RAY DIFFRACTIONr_scangle_it3.7714.5637
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 69 -
Rwork0.211 1332 -
all-1401 -
obs--99.64 %

+
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