[English] 日本語
Yorodumi
- PDB-2v0o: FCHO2 F-BAR domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2v0o
TitleFCHO2 F-BAR domain
ComponentsFCH DOMAIN ONLY PROTEIN 2
KeywordsLIPID BINDING PROTEIN / LIPID-BINDING PROTEIN / EFC DOMAIN / VESICLE TRAFFICKING / MEMBRANE CURVATURE / ENDOCYTOSIS / EXOCYTOSIS / F-BAR DOMAIN / POLYMORPHISM / LIPID- BINDING PROTEIN / COILED-COIL
Function / homology
Function and homology information


membrane invagination / clathrin coat assembly / clathrin-dependent endocytosis / clathrin-coated vesicle / phosphatidylserine binding / synaptic vesicle endocytosis / clathrin-coated pit / phosphatidylinositol-4,5-bisphosphate binding / phosphatidylinositol binding / protein localization to plasma membrane ...membrane invagination / clathrin coat assembly / clathrin-dependent endocytosis / clathrin-coated vesicle / phosphatidylserine binding / synaptic vesicle endocytosis / clathrin-coated pit / phosphatidylinositol-4,5-bisphosphate binding / phosphatidylinositol binding / protein localization to plasma membrane / Cargo recognition for clathrin-mediated endocytosis / presynapse / Clathrin-mediated endocytosis / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
F-BAR domain only protein 2 / : / GEM-interacting protein-like, FCH domain / Muniscin C-terminal / Muniscin C-terminal mu homology domain / Fes/CIP4, and EFC/F-BAR homology domain / Arfaptin homology (AH) domain/BAR domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain ...F-BAR domain only protein 2 / : / GEM-interacting protein-like, FCH domain / Muniscin C-terminal / Muniscin C-terminal mu homology domain / Fes/CIP4, and EFC/F-BAR homology domain / Arfaptin homology (AH) domain/BAR domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / Mu homology domain / Mu homology domain (MHD) profile. / AH/BAR domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / F-BAR domain only protein 2 / F-BAR domain only protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.3 Å
AuthorsHenne, W.M. / McMahon, H.T. / Kent, H.M. / Evans, P.R.
CitationJournal: Structure / Year: 2007
Title: Structure and Analysis of Fcho2 F-Bar Domain: A Dimerizing and Membrane Recruitment Module that Effects Membrane Curvature.
Authors: Henne, W.M. / Kent, H.M. / Ford, M.J.G. / Hedge, B.G. / Daumke, O. / Butler, P.J. / Mittal, R. / Langen, R. / Evans, P.R. / Mcmahon, H.T.
History
DepositionMay 15, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FCH DOMAIN ONLY PROTEIN 2
B: FCH DOMAIN ONLY PROTEIN 2
C: FCH DOMAIN ONLY PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7606
Polymers94,5833
Non-polymers1773
Water3,243180
1
A: FCH DOMAIN ONLY PROTEIN 2
B: FCH DOMAIN ONLY PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1744
Polymers63,0552
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: FCH DOMAIN ONLY PROTEIN 2
hetero molecules

C: FCH DOMAIN ONLY PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1744
Polymers63,0552
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)254.440, 65.680, 89.910
Angle α, β, γ (deg.)90.00, 110.32, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99957, -0.02891, -0.00502), (-0.02905, 0.9991, 0.03105), (0.00412, 0.03119, -0.99951)128.64897, 1.07341, 49.14447
2given(-0.76127, 0.01968, -0.64814), (-0.00427, -0.99967, -0.02534), (-0.64843, -0.01652, 0.7611)176.01089, 27.83235, 65.42796

-
Components

#1: Protein FCH DOMAIN ONLY PROTEIN 2 / FCHO2


Mass: 31527.719 Da / Num. of mol.: 3 / Fragment: F-BAR DOMAIN, RESIDUES 1-272
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS / References: UniProt: Q96CF5, UniProt: Q0JRZ9*PLUS
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsFIRST 4 RESIDUES LGSP ARE A CLONING ARTEFACT FROM THE PLASMID

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 66.97 % / Description: 2 SIMILAR HG DERIVATIVES
Crystal growpH: 9 / Details: 18% PEG4000, 300MM NA ACETATE, 100MM TRIS PH 9

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→45 Å / Num. obs: 61810 / % possible obs: 99.5 % / Observed criterion σ(I): -10 / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.2
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 1.6 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.3→119.52 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.909 / SU B: 13.472 / SU ML: 0.293 / Cross valid method: THROUGHOUT / ESU R: 0.301 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ASYMMETRIC UNIT CONTAINS 1.5 DIMERS, ONE COMPRISING CHAINS A & B, AND THE OTHER CHAIN C WHICH FORMS A DIMER WITH ITS SYMMETRY MATE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ASYMMETRIC UNIT CONTAINS 1.5 DIMERS, ONE COMPRISING CHAINS A & B, AND THE OTHER CHAIN C WHICH FORMS A DIMER WITH ITS SYMMETRY MATE RELATED BY THE SYMMETRY OPERATOR (1-X,Y,1-Z).
RfactorNum. reflection% reflectionSelection details
Rfree0.316 3140 5.1 %RANDOM
Rwork0.278 ---
obs0.28 58658 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.93 Å2
Baniso -1Baniso -2Baniso -3
1--6.45 Å20 Å2-2.42 Å2
2--0.37 Å20 Å2
3---4.4 Å2
Refinement stepCycle: LAST / Resolution: 2.3→119.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6565 0 12 180 6757
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0226677
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.7371.9518951
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7385813
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.98525.913323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.079151337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7311521
X-RAY DIFFRACTIONr_chiral_restr0.050.2990
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024900
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1520.23151
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.280.24745
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0980.2224
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.2108
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2411.54263
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.43426525
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.29432777
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.5094.52426
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.458 228
Rwork0.41 4305

+
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