[English] 日本語
Yorodumi
- PDB-6kyk: Crystal structure of Shank3 NTD-ANK mutant in complex with Rap1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kyk
TitleCrystal structure of Shank3 NTD-ANK mutant in complex with Rap1
Components
  • Ras-related protein Rap-1b
  • SH3 and multiple ankyrin repeat domains protein 3
KeywordsSTRUCTURAL PROTEIN/SIGNALING PROTEIN / Shank3 / GTPase / synaptic scaffold protein / STRUCTURAL PROTEIN-SIGNALING PROTEIN complex
Function / homology
Function and homology information


response to interleukin-17 / Neurexins and neuroligins / regulation of AMPA glutamate receptor clustering / guanylate kinase-associated protein clustering / striatal medium spiny neuron differentiation / synaptic receptor adaptor activity / positive regulation of glutamate receptor signaling pathway / postsynaptic density assembly / Rap protein signal transduction / embryonic epithelial tube formation ...response to interleukin-17 / Neurexins and neuroligins / regulation of AMPA glutamate receptor clustering / guanylate kinase-associated protein clustering / striatal medium spiny neuron differentiation / synaptic receptor adaptor activity / positive regulation of glutamate receptor signaling pathway / postsynaptic density assembly / Rap protein signal transduction / embryonic epithelial tube formation / NMDA glutamate receptor clustering / positive regulation of synapse structural plasticity / modification of postsynaptic structure / negative regulation of actin filament bundle assembly / vocal learning / negative regulation of cell volume / regulation of behavioral fear response / regulation of cell junction assembly / positive regulation of long-term neuronal synaptic plasticity / regulation of grooming behavior / structural constituent of postsynaptic density / AMPA glutamate receptor clustering / negative regulation of calcium ion-dependent exocytosis / positive regulation of integrin activation / vocalization behavior / negative regulation of synaptic vesicle exocytosis / RET signaling / neuron spine / calcium-ion regulated exocytosis / regulation of dendritic spine morphogenesis / neural precursor cell proliferation / locomotion / dendritic spine morphogenesis / Rap1 signalling / brain morphogenesis / establishment of endothelial barrier / regulation of establishment of cell polarity / regulation of long-term synaptic potentiation / MET activates RAP1 and RAC1 / positive regulation of AMPA receptor activity / long-term synaptic depression / regulation of postsynapse organization / positive regulation of dendritic spine development / exploration behavior / ciliary membrane / azurophil granule membrane / regulation of long-term synaptic depression / adult behavior / locomotory exploration behavior / p130Cas linkage to MAPK signaling for integrins / postsynaptic density, intracellular component / social behavior / positive regulation of excitatory postsynaptic potential / associative learning / GRB2:SOS provides linkage to MAPK signaling for Integrins / neuromuscular process controlling balance / excitatory synapse / glial cell proliferation / cellular response to cAMP / synapse assembly / ionotropic glutamate receptor binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / lipid droplet / Integrin signaling / positive regulation of synaptic transmission, glutamatergic / small monomeric GTPase / G protein activity / locomotory behavior / learning / long-term synaptic potentiation / G protein-coupled receptor binding / positive regulation of long-term synaptic potentiation / establishment of localization in cell / regulation of synaptic plasticity / modulation of chemical synaptic transmission / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / memory / SH3 domain binding / GDP binding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / : / MAPK cascade / cell-cell junction / Signaling by BRAF and RAF1 fusions / gene expression / actin binding / scaffold protein binding / cell population proliferation / dendritic spine / postsynaptic density / positive regulation of ERK1 and ERK2 cascade / learning or memory / neuron projection / GTPase activity / glutamatergic synapse / Neutrophil degranulation
Similarity search - Function
Ras-related protein Rap1 / PDZ domain 6 / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / Small GTPase, Ras-type / small GTPase Ras family profile. / SAM domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Sterile alpha motif. ...Ras-related protein Rap1 / PDZ domain 6 / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / Small GTPase, Ras-type / small GTPase Ras family profile. / SAM domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / Rab subfamily of small GTPases / 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 / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rap-1b / SH3 and multiple ankyrin repeat domains protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.82 Å
AuthorsCai, Q. / Zhang, M.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)AoE-M09-12 Hong Kong
CitationJournal: Structure / Year: 2020
Title: Shank3 Binds to and Stabilizes the Active Form of Rap1 and HRas GTPases via Its NTD-ANK Tandem with Distinct Mechanisms.
Authors: Cai, Q. / Hosokawa, T. / Zeng, M. / Hayashi, Y. / Zhang, M.
History
DepositionSep 19, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 18, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.3Nov 22, 2023Group: 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 / struct_ncs_dom_lim
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SH3 and multiple ankyrin repeat domains protein 3
B: SH3 and multiple ankyrin repeat domains protein 3
C: Ras-related protein Rap-1b
D: Ras-related protein Rap-1b
E: Ras-related protein Rap-1b
F: Ras-related protein Rap-1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,22714
Polymers160,0416
Non-polymers2,1868
Water1,31573
1
A: SH3 and multiple ankyrin repeat domains protein 3
C: Ras-related protein Rap-1b
D: Ras-related protein Rap-1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1137
Polymers80,0203
Non-polymers1,0934
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SH3 and multiple ankyrin repeat domains protein 3
E: Ras-related protein Rap-1b
F: Ras-related protein Rap-1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1137
Polymers80,0203
Non-polymers1,0934
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)171.032, 54.107, 203.110
Angle α, β, γ (deg.)90.000, 109.510, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13C
23E
14C
24F
15D
25E
16D
26F
17E
27F

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAPROPROAA6 - 36112 - 367
21ALAALAPROPROBB6 - 36112 - 367
12HISHISASNASNCC0 - 1663 - 169
22HISHISASNASNDD0 - 1663 - 169
13PROPROARGARGCC-1 - 1672 - 170
23PROPROARGARGEE-1 - 1672 - 170
14HISHISASNASNCC0 - 1663 - 169
24HISHISASNASNFF0 - 1663 - 169
15HISHISASNASNDD0 - 1663 - 169
25HISHISASNASNEE0 - 1663 - 169
16HISHISARGARGDD0 - 1673 - 170
26HISHISARGARGFF0 - 1673 - 170
17HISHISASNASNEE0 - 1663 - 169
27HISHISASNASNFF0 - 1663 - 169

NCS ensembles :
ID
1
2
3
4
5
6
7

-
Components

#1: Protein SH3 and multiple ankyrin repeat domains protein 3 / Shank3 / Proline-rich synapse-associated protein 2 / ProSAP2 / SPANK-2


Mass: 41394.734 Da / Num. of mol.: 2 / Fragment: NTD-ANK tandem / Mutation: L231R,F304Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Shank3, Kiaa1650, Prosap2 / Plasmid: pETM3C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4ACU6
#2: Protein
Ras-related protein Rap-1b / GTP-binding protein smg p21B


Mass: 19312.822 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAP1B, OK/SW-cl.11 / Plasmid: pSKB2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61224
#3: Chemical
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.56 % / Mosaicity: 0.711 ° / Mosaicity esd: 0.008 °
Crystal growTemperature: 289 K / Method: evaporation / pH: 8.5
Details: 0.1M bicine (pH8.5), 1% Dextran sulfate sodium salt, 5% PEG 20000, 10% PEG 1500

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 19, 2018
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.81→50 Å / Num. obs: 40063 / % possible obs: 94 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.065 / Rrim(I) all: 0.164 / Χ2: 0.726 / Net I/σ(I): 4.2 / Num. measured all: 242504
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.81-2.865.60.94818120.7570.4211.0420.43585.4
2.86-2.9160.93719210.7470.4021.0230.4291.9
2.91-2.976.40.7820000.8670.3230.8460.44294.2
2.97-3.036.40.66520210.8830.2750.7210.46196.7
3.03-3.096.30.52320660.9290.2160.5670.48597.5
3.09-3.166.30.49720740.9310.2060.5390.48296.8
3.16-3.246.30.39820310.9510.1680.4330.54598.6
3.24-3.336.30.3320920.9680.1380.3580.55698.3
3.33-3.436.20.28720680.9760.1210.3120.59797.9
3.43-3.546.20.26820780.9740.1140.2920.59898
3.54-3.674.60.23315550.9380.1130.2611.46173.5
3.67-3.815.40.19718540.9820.0880.2160.787.2
3.81-3.995.20.15219750.9830.070.1680.84794.1
3.99-4.25.60.11918910.9910.0530.1310.96787.7
4.2-4.466.10.10620520.9930.0460.1160.99495.2
4.46-4.86.30.09720790.9950.0420.1061.00697.9
4.8-5.296.50.09621090.9950.0410.1040.96998.3
5.29-6.056.60.09421200.9950.040.1020.9398.7
6.05-7.626.20.0821220.9940.0350.0871.11197.4
7.62-5060.06521430.9950.0290.0710.81494.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G4X, 4DXA

5g4x

4dxa


Resolution: 2.82→49 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.867 / WRfactor Rfree: 0.2772 / WRfactor Rwork: 0.2142 / FOM work R set: 0.6654 / SU B: 27.926 / SU ML: 0.489 / SU Rfree: 0.4776 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.478 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2998 1976 4.9 %RANDOM
Rwork0.2403 ---
obs0.2433 38087 93.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 191.43 Å2 / Biso mean: 66.375 Å2 / Biso min: 20.18 Å2
Baniso -1Baniso -2Baniso -3
1--2.81 Å2-0 Å2-1.72 Å2
2--8.87 Å20 Å2
3----3.87 Å2
Refinement stepCycle: final / Resolution: 2.82→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10982 0 132 73 11187
Biso mean--67.09 42.95 -
Num. residues----1390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01311338
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710338
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.64715364
X-RAY DIFFRACTIONr_angle_other_deg1.2011.58223982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.69851388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.90922.598662
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.416151958
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2041586
X-RAY DIFFRACTIONr_chiral_restr0.0560.21440
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212776
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022370
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A109940.11
12B109940.11
21C50940.12
22D50940.12
31C52200.11
32E52200.11
41C50730.13
42F50730.13
51D49600.14
52E49600.14
61D51930.11
62F51930.11
71E49300.15
72F49300.15
LS refinement shellResolution: 2.821→2.895 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 128 -
Rwork0.392 2341 -
all-2469 -
obs--78.31 %

+
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