[English] 日本語
Yorodumi
- PDB-1u5s: NMR structure of the complex between Nck-2 SH3 domain and PINCH-1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1u5s
TitleNMR structure of the complex between Nck-2 SH3 domain and PINCH-1 LIM4 domain
Components
  • Cytoplasmic protein NCK2Cytoplasm
  • PINCH protein
KeywordsMETAL BINDING PROTEIN / Protein-protein complex / beta barrel / beta sheet / zinc finger
Function / homology
Function and homology information


Regulation of cortical dendrite branching / negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / positive regulation of peptidyl-serine dephosphorylation / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / positive regulation of translation in response to endoplasmic reticulum stress / positive regulation of integrin-mediated signaling pathway / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / immunological synapse formation / dendritic spine development / Cell-extracellular matrix interactions ...Regulation of cortical dendrite branching / negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / positive regulation of peptidyl-serine dephosphorylation / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / positive regulation of translation in response to endoplasmic reticulum stress / positive regulation of integrin-mediated signaling pathway / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / immunological synapse formation / dendritic spine development / Cell-extracellular matrix interactions / cytoskeletal anchor activity / vesicle membrane / cell-cell junction organization / signal complex assembly / Activation of RAC1 / positive regulation of cell-substrate adhesion / Nephrin family interactions / Ephrin signaling / lamellipodium assembly / RHOV GTPase cycle / positive regulation of actin filament polymerization / negative regulation of PERK-mediated unfolded protein response / positive regulation of focal adhesion assembly / RHOU GTPase cycle / ephrin receptor signaling pathway / signaling adaptor activity / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of T cell proliferation / cellular response to transforming growth factor beta stimulus / tumor necrosis factor-mediated signaling pathway / T cell activation / phosphotyrosine residue binding / Downstream signal transduction / actin filament organization / establishment of protein localization / epidermal growth factor receptor signaling pathway / receptor tyrosine kinase binding / positive regulation of GTPase activity / VEGFA-VEGFR2 Pathway / cell-cell adhesion / cell-cell junction / signaling receptor complex adaptor activity / cell migration / scaffold protein binding / positive regulation of canonical NF-kappaB signal transduction / postsynaptic density / negative regulation of cell population proliferation / focal adhesion / negative regulation of DNA-templated transcription / protein-containing complex binding / positive regulation of gene expression / protein kinase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / signal transduction / positive regulation of transcription by RNA polymerase II / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Nck2, SH3 domain 1 / Nck2, SH3 domain 2 / Nck2, SH3 domain 3 / Nck2, SH2 domain / : / : / Cytoplasmic protein NCK / Cysteine Rich Protein / Cysteine Rich Protein / LIM zinc-binding domain signature. ...Nck2, SH3 domain 1 / Nck2, SH3 domain 2 / Nck2, SH3 domain 3 / Nck2, SH2 domain / : / : / Cytoplasmic protein NCK / Cysteine Rich Protein / Cysteine Rich Protein / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / Variant SH3 domain / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. / Src homology 3 domains / SH2 domain superfamily / Ribbon / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Cytoplasmic protein NCK2 / LIM and senescent cell antigen-like-containing domain protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics, rigid body, torsion angle dynamics
AuthorsVaynberg, J. / Fukuda, T. / Vinogradova, O. / Velyvis, A. / Ng, L. / Wu, C. / Qin, J.
CitationJournal: Mol.Cell / Year: 2005
Title: Structure of an ultraweak protein-protein complex and its crucial role in regulation of cell morphology and motility.
Authors: Vaynberg, J. / Fukuda, T. / Chen, K. / Vinogradova, O. / Velyvis, A. / Tu, Y. / Ng, L. / Wu, C. / Qin, J.
History
DepositionJul 28, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytoplasmic protein NCK2
B: PINCH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7274
Polymers15,5962
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / 50structures with the most reperesentative side chains orientations on the complex interface
RepresentativeModel #1closest to the average

-
Components

#1: Protein Cytoplasmic protein NCK2 / Cytoplasm / NCK adaptor protein 2 / SH2/SH3 adaptor protein NCK-beta / Nck-2


Mass: 8063.068 Da / Num. of mol.: 1 / Fragment: third SH3 domain (residues 192-262)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCK2 / Plasmid: pTYB11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O43639
#2: Protein PINCH protein / Particularly interesting new Cys-His protein / LIM and senescent cell antigen-like domains 1


Mass: 7532.742 Da / Num. of mol.: 1 / Fragment: fourth LIM domain (residues 188-251)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIMS1 / Plasmid: pGex-4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P48059
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 13C-separated NOESY
1313D 15N-separated NOESY
1423D 15N-separated NOESY
15115N/13C-edited 15N,13C-separated NOESY
16215N/13C-edited 15N,13C-separated NOESY
NMR detailsText: The structures of free form SH3 and LIM4 domains were determined using triple-resonance NMR spectroscopy

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.0mM LIM4 of PINCH-1 U-15N,13C, 1.5mM SH3-3 of Nck-2 unlabeled, 25mM Phosphate buffer, 100mM NaCl, 0.1mM TCEP, 90% H2O, 10% D2O90% H2O/10% D2O
20.6mM SH3-3 of Nck-2 U-15N,13C, 2.5mM LIM4 of PINCH-1, 25mM Phosphate buffer, 100mM NaCl, 0.1mM TCEP, 90% H2O, 10% D2O90% H2O/10% D2O
31.3mM SH3-3 of Nck-2 U-15N,13C, 25mM Phosphate buffer, 100mM NaCl, 0.1mM TCEP, 90% H2O, 10% D2O90% H2O/10% D2O
41.7mM LIM4 of PINCH-1, U-15N,13C 25mM Phosphate buffer, 100mM NaCl, 0.1mM TCEP, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
VNMRcollection
NMRPipeDelagliodata analysis
X-PLOR3.1Brungerstructure solution
Xplor-NIHClorestructure solution
Xplor-NIHClorerefinement
RefinementMethod: simulated annealing, molecular dynamics, rigid body, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the most reperesentative side chains orientations on the complex interface
Conformers calculated total number: 50 / Conformers submitted total number: 18

+
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