[English] 日本語
Yorodumi
- PDB-7kqq: Crystal structure of human WDR55 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kqq
TitleCrystal structure of human WDR55
ComponentsWD repeat-containing protein 55
KeywordsNUCLEAR PROTEIN / WDR55 / WD-repeat / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


rRNA processing / nucleolus / nucleoplasm / cytoplasm
Similarity search - Function
WD repeat protein 55 / WDR55 / : / Anaphase-promoting complex subunit 4 WD40 domain / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats ...WD repeat protein 55 / WDR55 / : / Anaphase-promoting complex subunit 4 WD40 domain / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
WD repeat-containing protein 55
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZeng, H. / Hutchinson, A. / Li, Y. / Seitova, A. / Edwards, A.M. / Arrowsmith, C.H. / Halabelian, L. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of human WDR55
Authors: Zeng, H. / Hutchinson, A. / Li, Y. / Seitova, A. / Edwards, A.M. / Arrowsmith, C.H. / Halabelian, L. / Structural Genomics Consortium (SGC)
History
DepositionNov 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: WD repeat-containing protein 55
B: WD repeat-containing protein 55
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,99013
Polymers68,7022
Non-polymers1,28911
Water5,296294
1
A: WD repeat-containing protein 55
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9376
Polymers34,3511
Non-polymers5865
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: WD repeat-containing protein 55
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0547
Polymers34,3511
Non-polymers7036
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.976, 58.599, 88.231
Angle α, β, γ (deg.)90.000, 95.480, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein WD repeat-containing protein 55


Mass: 34350.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR55 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9H6Y2
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 117.146 Da / Num. of mol.: 11 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% W/V PEG 3350, 0.2 M Potassium Thiocyanate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.8→48.75 Å / Num. obs: 72091 / % possible obs: 96.9 % / Redundancy: 3.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.045 / Rrim(I) all: 0.085 / Net I/σ(I): 8.2 / Num. measured all: 234127 / Scaling rejects: 300
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.4 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.840.5671488844110.7050.3560.6731.499.5
9-48.750.03819685750.9960.0230.04518.190.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TBG

1tbg


Resolution: 1.8→48.75 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.2481 / WRfactor Rwork: 0.201 / FOM work R set: 0.823 / SU B: 2.902 / SU ML: 0.087 / SU R Cruickshank DPI: 0.1117 / SU Rfree: 0.1168 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2333 3485 4.8 %RANDOM
Rwork0.1878 ---
obs0.19 68592 96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.23 Å2 / Biso mean: 33.375 Å2 / Biso min: 4.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å2-0 Å2-0.18 Å2
2--1.11 Å2-0 Å2
3----0.56 Å2
Refinement stepCycle: final / Resolution: 1.8→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4614 0 11 294 4919
Biso mean--32.08 40.8 -
Num. residues----609
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134801
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174506
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.6316514
X-RAY DIFFRACTIONr_angle_other_deg1.3621.58210385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7325631
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.51621.52250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2415808
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4261539
X-RAY DIFFRACTIONr_chiral_restr0.0760.2622
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025540
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021094
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 251 -
Rwork0.311 5225 -
all-5476 -
obs--99.35 %

+
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