[English] 日本語
Yorodumi
- PDB-6amb: Crystal Structure of the Afadin RA1 domain in complex with HRAS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6amb
TitleCrystal Structure of the Afadin RA1 domain in complex with HRAS
Components
  • Afadin
  • GTPase HRas
KeywordsSIGNALING PROTEIN / GTPase / adhesion / RA domain / RBD domain
Function / homology
Function and homology information


regulation of oligodendrocyte progenitor proliferation / radial glial cell differentiation / adherens junction maintenance / establishment of protein localization to plasma membrane / regulation of postsynapse assembly / protein localization to cell junction / pore complex assembly / Adherens junctions interactions / dendrite arborization / LIM domain binding ...regulation of oligodendrocyte progenitor proliferation / radial glial cell differentiation / adherens junction maintenance / establishment of protein localization to plasma membrane / regulation of postsynapse assembly / protein localization to cell junction / pore complex assembly / Adherens junctions interactions / dendrite arborization / LIM domain binding / telencephalon development / neuroepithelial cell differentiation / cell-cell adhesion mediated by cadherin / positive regulation of dendritic spine morphogenesis / positive regulation of dendrite extension / brain morphogenesis / GTPase complex / oncogene-induced cell senescence / positive regulation of mini excitatory postsynaptic potential / positive regulation of ruffle assembly / positive regulation of dendrite morphogenesis / negative regulation of GTPase activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / apical junction complex / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of wound healing / pore complex / defense response to protozoan / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RAS signaling downstream of NF1 loss-of-function variants / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / homeostasis of number of cells / SHC1 events in ERBB4 signaling / positive regulation of protein targeting to membrane / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / adipose tissue development / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / : / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / Schwann cell development / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / presynaptic active zone membrane / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR4 signaling / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / cell adhesion molecule binding / Signaling by FGFR2 in disease / somatodendritic compartment / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EPHB-mediated forward signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / Ras activation upon Ca2+ influx through NMDA receptor / myelination / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / CD209 (DC-SIGN) signaling / NCAM signaling for neurite out-growth / SHC1 events in ERBB2 signaling / hippocampal mossy fiber to CA3 synapse / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / intrinsic apoptotic signaling pathway / small monomeric GTPase / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / G protein activity / positive regulation of epithelial cell proliferation / positive regulation of GTPase activity / VEGFR2 mediated cell proliferation / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / adherens junction / animal organ morphogenesis / positive regulation of JNK cascade / Signaling by ERBB2 TMD/JMD mutants / RAF activation
Similarity search - Function
: / Afadin, cargo binding domain / Ras association (RalGDS/AF-6) domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain ...: / Afadin, cargo binding domain / Ras association (RalGDS/AF-6) domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / Forkhead associated domain / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Small GTPase, Ras-type / small GTPase Ras family profile. / PDZ domain / 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 / PDZ superfamily / Rab subfamily of small GTPases / Small GTP-binding protein domain / Ubiquitin-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase HRas / Afadin
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSmith, M.J. / Ishiyama, N. / Ikura, M.
CitationJournal: Nat Commun / Year: 2017
Title: Evolution of AF6-RAS association and its implications in mixed-lineage leukemia.
Authors: Smith, M.J. / Ottoni, E. / Ishiyama, N. / Goudreault, M. / Haman, A. / Meyer, C. / Tucholska, M. / Gasmi-Seabrook, G. / Menezes, S. / Laister, R.C. / Minden, M.D. / Marschalek, R. / Gingras, ...Authors: Smith, M.J. / Ottoni, E. / Ishiyama, N. / Goudreault, M. / Haman, A. / Meyer, C. / Tucholska, M. / Gasmi-Seabrook, G. / Menezes, S. / Laister, R.C. / Minden, M.D. / Marschalek, R. / Gingras, A.C. / Hoang, T. / Ikura, M.
History
DepositionAug 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GTPase HRas
B: Afadin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4624
Polymers30,9162
Non-polymers5472
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-14 kcal/mol
Surface area12970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.239, 57.152, 73.329
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein GTPase HRas / H-Ras-1 / Ha-Ras / Transforming protein p21 / c-H-ras / p21ras


Mass: 19386.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P01112
#2: Protein Afadin / Afadin adherens junction formation factor / Protein Af-6


Mass: 11529.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Afdn, Af6, Mllt4 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9QZQ1
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#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.: 10 / 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: 1.63 Å3/Da / Density % sol: 24.76 %
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 8.9 / Details: PEG3350, K2HPO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 7437 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.041 / Rrim(I) all: 0.106 / Χ2: 0.993 / Net I/σ(I): 8.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.546.20.5573580.8530.2410.6090.756100
2.54-2.596.90.5563660.9010.2280.6020.82999.7
2.59-2.647.10.4793480.930.1930.5170.819100
2.64-2.697.10.4423810.9170.1760.4760.889100
2.69-2.757.10.4583620.9150.1850.4950.894100
2.75-2.827.10.3553680.9270.1430.3830.9100
2.82-2.897.10.2863590.9510.1150.3081.011100
2.89-2.967.10.2523580.960.1020.2721.074100
2.96-3.0570.2083670.9860.0840.2251.035100
3.05-3.1570.1633630.9880.0660.1771.109100
3.15-3.2670.1483700.9890.060.161.057100
3.26-3.3970.1353680.9890.0550.1461.147100
3.39-3.5570.1153670.9910.0470.1241.2100
3.55-3.7370.13740.9940.0410.1081.099100
3.73-3.976.90.0833660.9950.0340.091.078100
3.97-4.276.90.0763730.9960.0310.0820.993100
4.27-4.76.80.0673850.9970.0280.0730.963100
4.7-5.386.60.0673870.9970.0280.0730.974100
5.38-6.786.40.0683900.9960.0290.0740.961100
6.78-505.90.0694270.9960.0310.0761.02798.8

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DDC

3ddc


Resolution: 2.5→40.301 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.51
RfactorNum. reflection% reflection
Rfree0.2655 725 10.03 %
Rwork0.2184 --
obs0.2232 7226 97.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 110.91 Å2 / Biso mean: 54.2805 Å2 / Biso min: 27.18 Å2
Refinement stepCycle: final / Resolution: 2.5→40.301 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1967 0 33 10 2010
Biso mean--38.51 45.2 -
Num. residues----249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022037
X-RAY DIFFRACTIONf_angle_d0.5222758
X-RAY DIFFRACTIONf_chiral_restr0.041311
X-RAY DIFFRACTIONf_plane_restr0.003351
X-RAY DIFFRACTIONf_dihedral_angle_d17.4411223
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4991-2.6920.33381340.23831200133493
2.692-2.96290.40711420.25741255139796
2.9629-3.39140.26971450.23231307145299
3.3914-4.27210.26061470.209513271474100
4.2721-40.30590.22471570.20714121569100

+
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://pdbjlc1.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