[English] 日本語
Yorodumi
- PDB-4l6y: Structure of the microtubule associated protein PRC1 (Protein Reg... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4l6y
TitleStructure of the microtubule associated protein PRC1 (Protein Regulator of Cytokinesis 1)
ComponentsProtein regulator of cytokinesis 1
KeywordsSTRUCTURAL PROTEIN / Spectrin / Microtubule binding / microtubule crosslinking / microtubule / kinesin-4 / spindle midzone
Function / homology
Function and homology information


contractile ring / mitotic spindle midzone / mitotic spindle elongation / mitotic spindle midzone assembly / RHO GTPases activate CIT / kinesin binding / intercellular bridge / regulation of cytokinesis / spindle microtubule / microtubule cytoskeleton organization ...contractile ring / mitotic spindle midzone / mitotic spindle elongation / mitotic spindle midzone assembly / RHO GTPases activate CIT / kinesin binding / intercellular bridge / regulation of cytokinesis / spindle microtubule / microtubule cytoskeleton organization / spindle / spindle pole / chromosome / microtubule cytoskeleton / midbody / microtubule binding / cell division / positive regulation of cell population proliferation / protein kinase binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Microtubule-associated protein, MAP65/Ase1/PRC1 / Microtubule associated protein (MAP65/ASE1 family)
Similarity search - Domain/homology
Protein regulator of cytokinesis 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3015 Å
AuthorsSubramanian, R. / Ti, S. / Tan, L. / Darst, S.A. / Kapoor, T.M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: Marking and Measuring Single Microtubules by PRC1 and Kinesin-4.
Authors: Subramanian, R. / Ti, S.C. / Tan, L. / Darst, S.A. / Kapoor, T.M.
History
DepositionJun 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein regulator of cytokinesis 1
B: Protein regulator of cytokinesis 1


Theoretical massNumber of molelcules
Total (without water)116,3652
Polymers116,3652
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-45 kcal/mol
Surface area55530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.660, 209.800, 113.410
Angle α, β, γ (deg.)90.00, 105.64, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Protein regulator of cytokinesis 1


Mass: 58182.660 Da / Num. of mol.: 2 / Fragment: UNP Residues 1-486
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRC1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Rosetta / References: UniProt: O43663

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 6.3 Å3/Da / Density % sol: 80.5 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Concentration: 5-10 mg/ml. Protein buffer: 80 mM PIPES (pH 6.8), 1 mM MgCl2, 1 mM EGTA, 150 mM KCl, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 1, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection twinOperator: h,-k,-h-l / Fraction: 0.5
ReflectionResolution: 3.2→40 Å / Num. all: 40830 / Num. obs: 39522 / % possible obs: 90.5 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 1.4
Reflection shellResolution: 3.2→3.31 Å / % possible all: 82.2

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASER(phenix)phasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4L3I

4l3i


Resolution: 3.3015→29.906 Å / σ(F): 1.37 / Phase error: 35.46 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.3064 2001 5.4 %
Rwork0.2754 --
obs0.2762 37064 90.53 %
all-37064 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3015→29.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6550 0 0 0 6550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036637
X-RAY DIFFRACTIONf_angle_d0.6329000
X-RAY DIFFRACTIONf_dihedral_angle_d11.8942370
X-RAY DIFFRACTIONf_chiral_restr0.0421063
X-RAY DIFFRACTIONf_plane_restr0.0031174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3015-3.39070.4331410.34492569X-RAY DIFFRACTION82
3.3907-3.49030.30731440.32052621X-RAY DIFFRACTION85
3.4903-3.60270.36991390.30132697X-RAY DIFFRACTION85
3.6027-3.73130.34731430.29822733X-RAY DIFFRACTION87
3.7313-3.88030.30021410.28782766X-RAY DIFFRACTION88
3.8803-4.05650.30531470.27972817X-RAY DIFFRACTION88
4.0565-4.26970.30051390.26782719X-RAY DIFFRACTION88
4.2697-4.53630.35521480.27372773X-RAY DIFFRACTION88
4.5363-4.88510.32221430.26852738X-RAY DIFFRACTION87
4.8851-5.3740.31751400.27332726X-RAY DIFFRACTION87
5.374-6.14530.40311370.38312712X-RAY DIFFRACTION86
6.1453-7.71870.29911460.31722674X-RAY DIFFRACTION85
7.7187-29.20810.20771410.18372624X-RAY DIFFRACTION82

+
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