[English] 日本語
Yorodumi
- PDB-4wpe: Crystal Structure of Hof1p F-BAR domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wpe
TitleCrystal Structure of Hof1p F-BAR domain
ComponentsCytokinesis protein 2
KeywordsPROTEIN BINDING / F-BAR domain / membrane
Function / homology
Function and homology information


primary cell septum biogenesis / protein localization to cell division site / negative regulation of formin-nucleated actin cable assembly / HICS complex / regulation of mitotic actomyosin contractile ring contraction / : / mitotic actomyosin contractile ring maturation / MIH complex / protein localization to cell division site involved in mitotic actomyosin contractile ring assembly / Clathrin-mediated endocytosis ...primary cell septum biogenesis / protein localization to cell division site / negative regulation of formin-nucleated actin cable assembly / HICS complex / regulation of mitotic actomyosin contractile ring contraction / : / mitotic actomyosin contractile ring maturation / MIH complex / protein localization to cell division site involved in mitotic actomyosin contractile ring assembly / Clathrin-mediated endocytosis / mitotic actomyosin contractile ring, proximal layer / myosin II heavy chain binding / cellular bud neck septin ring / mitotic actomyosin contractile ring assembly / cellular bud neck contractile ring / site of polarized growth / actomyosin contractile ring / cellular bud neck / cell division site / mitotic cytokinesis / cytoskeletal protein binding / phospholipid binding / cell cortex / cytoskeleton / protein-containing complex binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Arfaptin homology (AH) domain/BAR domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Src homology 3 domains / SH3-like domain superfamily ...Arfaptin homology (AH) domain/BAR domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Cytokinesis protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsLemmon, M.A. / Moravcevic, K.
CitationJournal: Structure / Year: 2015
Title: Comparison of Saccharomyces cerevisiae F-BAR Domain Structures Reveals a Conserved Inositol Phosphate Binding Site.
Authors: Moravcevic, K. / Alvarado, D. / Schmitz, K.R. / Kenniston, J.A. / Mendrola, J.M. / Ferguson, K.M. / Lemmon, M.A.
History
DepositionOct 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_radiation_wavelength / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytokinesis protein 2


Theoretical massNumber of molelcules
Total (without water)36,0951
Polymers36,0951
Non-polymers00
Water72140
1
A: Cytokinesis protein 2

A: Cytokinesis protein 2


Theoretical massNumber of molelcules
Total (without water)72,1902
Polymers72,1902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area7960 Å2
ΔGint-62 kcal/mol
Surface area27860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.178, 43.893, 95.858
Angle α, β, γ (deg.)90.00, 133.53, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-417-

HOH

-
Components

#1: Protein Cytokinesis protein 2 / / Homolog of CDC15 protein 1


Mass: 36095.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: HOF1, CYK2, YMR032W, YM9973.05 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q05080
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.17 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Na citrate, pH 5.5, containing 0.1 M ammonium acetate, and 5-7% (w/v) PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 5, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 11489 / % possible obs: 98.9 % / Redundancy: 7.2 % / Net I/σ(I): 33.9

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementResolution: 2.7→39.908 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2466 546 4.78 %
Rwork0.2084 --
obs0.2104 11429 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→39.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2178 0 0 40 2218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032221
X-RAY DIFFRACTIONf_angle_d0.6072988
X-RAY DIFFRACTIONf_dihedral_angle_d15.425815
X-RAY DIFFRACTIONf_chiral_restr0.023328
X-RAY DIFFRACTIONf_plane_restr0.002387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6995-2.9710.31421370.24962545X-RAY DIFFRACTION94
2.971-3.40080.34811320.25492747X-RAY DIFFRACTION99
3.4008-4.28380.23111430.19442752X-RAY DIFFRACTION100
4.2838-39.91190.20351340.19192839X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 23.3817 Å / Origin y: 39.7422 Å / Origin z: 61.4186 Å
111213212223313233
T0.3968 Å2-0.1109 Å2-0.0018 Å2-0.6041 Å2-0.1177 Å2--0.4414 Å2
L-0.0161 °2-0.1199 °2-0.225 °2-0.0341 °2-0.178 °2--0.2811 °2
S-0.1144 Å °0.1975 Å °-0.0118 Å °-0.0059 Å °-0.1456 Å °0.0413 Å °0.0771 Å °-0.0257 Å °-0.0196 Å °
Refinement TLS groupSelection details: all

+
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