[English] 日本語
Yorodumi
- PDB-5g4x: The crystal structure of the SHANK3 N-terminus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5g4x
TitleThe crystal structure of the SHANK3 N-terminus
ComponentsSH3 AND MULTIPLE ANKYRIN REPEAT DOMAINS PROTEIN 3
KeywordsSTRUCTURAL PROTEIN / SHANK3 / RAS / INTEGRIN.
Function / homology
Function and homology information


response to interleukin-17 / regulation of AMPA glutamate receptor clustering / guanylate kinase-associated protein clustering / striatal medium spiny neuron differentiation / synaptic receptor adaptor activity / maintenance of postsynaptic density structure / RET signaling / positive regulation of glutamate receptor signaling pathway / postsynaptic density assembly / embryonic epithelial tube formation ...response to interleukin-17 / regulation of AMPA glutamate receptor clustering / guanylate kinase-associated protein clustering / striatal medium spiny neuron differentiation / synaptic receptor adaptor activity / maintenance of postsynaptic density structure / RET signaling / positive regulation of glutamate receptor signaling pathway / postsynaptic density assembly / embryonic epithelial tube formation / Neurexins and neuroligins / positive regulation of synapse structural plasticity / negative regulation of actin filament bundle assembly / vocal learning / negative regulation of cell volume / positive regulation of long-term neuronal synaptic plasticity / structural constituent of postsynaptic density / regulation of grooming behavior / NMDA glutamate receptor clustering / vocalization behavior / regulation of dendritic spine morphogenesis / regulation of behavioral fear response / neuron spine / AMPA glutamate receptor clustering / neural precursor cell proliferation / locomotion / dendritic spine morphogenesis / brain morphogenesis / regulation of long-term synaptic potentiation / positive regulation of AMPA receptor activity / long-term synaptic depression / regulation of postsynapse organization / ciliary membrane / exploration behavior / regulation of long-term synaptic depression / adult behavior / positive regulation of dendritic spine development / locomotory exploration behavior / postsynaptic density, intracellular component / social behavior / associative learning / positive regulation of excitatory postsynaptic potential / neuromuscular process controlling balance / glial cell proliferation / synapse assembly / ionotropic glutamate receptor binding / positive regulation of synaptic transmission, glutamatergic / locomotory behavior / learning / long-term synaptic potentiation / positive regulation of long-term synaptic potentiation / G protein-coupled receptor binding / regulation of synaptic plasticity / modulation of chemical synaptic transmission / memory / SH3 domain binding / : / MAPK cascade / gene expression / actin binding / scaffold protein binding / dendritic spine / postsynaptic density / learning or memory / neuron projection / glutamatergic synapse / protein-containing complex binding / zinc ion binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
PDZ domain 6 / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. ...PDZ domain 6 / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / Ankyrin repeats (3 copies) / PDZ superfamily / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
SH3 and multiple ankyrin repeat domains protein 3
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.166 Å
AuthorsZacharchenko, T. / Barsukov, I.
CitationJournal: Nat. Cell Biol. / Year: 2017
Title: SHANK proteins limit integrin activation by directly interacting with Rap1 and R-Ras.
Authors: Lilja, J. / Zacharchenko, T. / Georgiadou, M. / Jacquemet, G. / Franceschi, N. / Peuhu, E. / Hamidi, H. / Pouwels, J. / Martens, V. / Nia, F.H. / Beifuss, M. / Boeckers, T. / Kreienkamp, H.J. ...Authors: Lilja, J. / Zacharchenko, T. / Georgiadou, M. / Jacquemet, G. / Franceschi, N. / Peuhu, E. / Hamidi, H. / Pouwels, J. / Martens, V. / Nia, F.H. / Beifuss, M. / Boeckers, T. / Kreienkamp, H.J. / Barsukov, I.L. / Ivaska, J.
History
DepositionMay 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Apr 12, 2017Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SH3 AND MULTIPLE ANKYRIN REPEAT DOMAINS PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,49431
Polymers38,6321
Non-polymers1,86230
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.760, 86.760, 158.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein SH3 AND MULTIPLE ANKYRIN REPEAT DOMAINS PROTEIN 3 / SHANK3 / PROLINE-RICH SYNAPSE-ASSOCIATED PROTEIN 2 / PROSAP2 / SPANK-2 / SHANK3


Mass: 38631.645 Da / Num. of mol.: 1 / Fragment: SPN-ARR, RESIDUES 1-348 / Source method: isolated from a natural source / Source: (natural) RATTUS NORVEGICUS (Norway rat) / References: UniProt: Q9JLU4
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 3.81 Å3/Da / Density % sol: 67 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1M HEPES PH 7.5, 0.4M K/NA TARTRATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Dec 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.16→48.54 Å / Num. obs: 32995 / % possible obs: 100 % / Observed criterion σ(I): 4 / Redundancy: 12.2 % / Biso Wilson estimate: 34.17 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.7
Reflection shellResolution: 2.17→2.3 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 4.4 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N11

1n11


Resolution: 2.166→48.538 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 16.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1857 1671 5.1 %
Rwork0.1626 --
obs0.1638 32995 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.166→48.538 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2699 0 120 258 3077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112866
X-RAY DIFFRACTIONf_angle_d0.9883831
X-RAY DIFFRACTIONf_dihedral_angle_d12.721704
X-RAY DIFFRACTIONf_chiral_restr0.058415
X-RAY DIFFRACTIONf_plane_restr0.007504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1661-2.22980.21661440.19212572X-RAY DIFFRACTION100
2.2298-2.30180.20921130.18052561X-RAY DIFFRACTION100
2.3018-2.38410.21531420.17082555X-RAY DIFFRACTION100
2.3841-2.47950.17581410.16422579X-RAY DIFFRACTION100
2.4795-2.59240.22371360.16662538X-RAY DIFFRACTION100
2.5924-2.7290.221580.16442581X-RAY DIFFRACTION100
2.729-2.90.1871380.1712586X-RAY DIFFRACTION100
2.9-3.12390.24151170.17182619X-RAY DIFFRACTION100
3.1239-3.43810.18821500.16922596X-RAY DIFFRACTION100
3.4381-3.93550.15561450.16122637X-RAY DIFFRACTION100
3.9355-4.95750.16031380.14182672X-RAY DIFFRACTION100
4.9575-48.55010.17811490.16192828X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.123-0.22480.67293.6522-0.44525.87090.1591-0.04110.3507-0.4329-0.08670.1652-0.8674-0.7564-0.00170.45720.15920.14680.3790.13890.432272.36250.023452.126
24.41271.12660.08671.2399-0.24450.90710.14040.02170.0204-0.0479-0.12670.05810.1124-0.0303-0.00970.23040.0358-0.00730.159-0.03940.177755.911834.920371.4042
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 2 THROUGH 112 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 113 THROUGH 347 )

+
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