[English] 日本語
Yorodumi
- PDB-5nv1: SH3 domain from Mouse cortactin (C 2 2 21 crystal form) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nv1
TitleSH3 domain from Mouse cortactin (C 2 2 21 crystal form)
ComponentsSrc substrate cortactin
KeywordsSIGNALING PROTEIN / SH3 domain / cortactin / signaling / cancer / invadopodium
Function / homology
Function and homology information


lamellipodium organization / site of polarized growth / Arp2/3 complex binding / modification of postsynaptic actin cytoskeleton / modification of postsynaptic structure / mitotic spindle midzone / regulation of cell projection assembly / regulation of mitophagy / postsynaptic actin cytoskeleton / profilin binding ...lamellipodium organization / site of polarized growth / Arp2/3 complex binding / modification of postsynaptic actin cytoskeleton / modification of postsynaptic structure / mitotic spindle midzone / regulation of cell projection assembly / regulation of mitophagy / postsynaptic actin cytoskeleton / profilin binding / positive regulation of smooth muscle contraction / regulation of actin filament polymerization / positive regulation of chemotaxis / substrate-dependent cell migration, cell extension / focal adhesion assembly / podosome / proline-rich region binding / dendritic spine maintenance / regulation of axon extension / cortical actin cytoskeleton / cortical cytoskeleton / positive regulation of actin filament polymerization / extrinsic apoptotic signaling pathway / clathrin-coated pit / voltage-gated potassium channel complex / ruffle / neuron projection morphogenesis / receptor-mediated endocytosis / cell motility / actin filament / negative regulation of extrinsic apoptotic signaling pathway / intracellular protein transport / actin filament binding / cell junction / lamellipodium / cell cortex / actin cytoskeleton organization / postsynapse / dendritic spine / focal adhesion / glutamatergic synapse / Golgi apparatus / endoplasmic reticulum / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Hs1/Cortactin / Cortactin, SH3 domain / Repeat in HS1/Cortactin / Cortactin repeat profile. / Variant SH3 domain / SH3 Domains / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. ...Hs1/Cortactin / Cortactin, SH3 domain / Repeat in HS1/Cortactin / Cortactin repeat profile. / Variant SH3 domain / SH3 Domains / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Src substrate cortactin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsTwafra, S. / Dessau, M.
CitationJournal: To Be Published
Title: SH3 domain from Mouse cortactin (C 2 2 21 crystal form)
Authors: Twafra, S. / Gil-Henn, H. / Dessau, M.
History
DepositionMay 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Src substrate cortactin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1144
Polymers6,8031
Non-polymers3123
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-4 kcal/mol
Surface area4060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.360, 55.950, 50.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Src substrate cortactin


Mass: 6802.532 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cttn, Ems1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q60598
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.13 Å3/Da / Density % sol: 42.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.6 M Mg-sulfate, 0.1 M MES pH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.007997 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007997 Å / Relative weight: 1
ReflectionResolution: 1.51→33.2 Å / Num. obs: 9248 / % possible obs: 98.3 % / Redundancy: 6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.51
Reflection shellResolution: 1.51→1.58 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.831 / % possible all: 96.5

-
Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X69

1x69


Resolution: 1.51→33.2 Å / Cross valid method: FREE R-VALUE /
Num. reflection% reflection
obs9223 98.3 %
Displacement parametersBiso max: 139.35 Å2 / Biso mean: 25.9728 Å2 / Biso min: 8.35 Å2
Refinement stepCycle: LAST / Resolution: 1.51→33.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms479 0 19 67 565

+
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://pdbjlvh1.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