[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 / protein localization to cell junction / Adherens junctions interactions / pore complex assembly / neuroepithelial cell differentiation / telencephalon development / cell-cell adhesion mediated by cadherin ...regulation of oligodendrocyte progenitor proliferation / radial glial cell differentiation / adherens junction maintenance / establishment of protein localization to plasma membrane / protein localization to cell junction / Adherens junctions interactions / pore complex assembly / neuroepithelial cell differentiation / telencephalon development / cell-cell adhesion mediated by cadherin / phospholipase C activator activity / brain morphogenesis / GTPase complex / positive regulation of ruffle assembly / oncogene-induced cell senescence / negative regulation of GTPase activity / positive regulation of miRNA metabolic process / T-helper 1 type immune response / apical junction complex / positive regulation of wound healing / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / defense response to protozoan / pore complex / 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 / regulation of postsynapse assembly / SOS-mediated signalling / homeostasis of number of cells / Activated NTRK3 signals through RAS / positive regulation of protein targeting to membrane / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / adipose tissue development / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Schwann cell development / SHC-mediated cascade:FGFR2 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / 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 / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / protein-membrane adaptor activity / cell adhesion molecule binding / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / presynaptic active zone membrane / Signaling by FGFR3 in disease / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EPHB-mediated forward signaling / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / myelination / EGFR Transactivation by Gastrin / positive regulation of GTPase activity / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / positive regulation of MAP kinase activity / GRB2 events in ERBB2 signaling / Downstream signal transduction / Ras activation upon Ca2+ influx through NMDA receptor / SHC1 events in ERBB2 signaling / Insulin receptor signalling cascade / intrinsic apoptotic signaling pathway / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / hippocampal mossy fiber to CA3 synapse / VEGFR2 mediated cell proliferation / positive regulation of epithelial cell proliferation / small monomeric GTPase / animal organ morphogenesis / adherens junction / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / positive regulation of JNK cascade / RAF activation / regulation of long-term neuronal synaptic plasticity / Signaling by ERBB2 TMD/JMD mutants / Signaling by high-kinase activity BRAF mutants / Signaling by SCF-KIT / postsynaptic density membrane / Constitutive Signaling by EGFRvIII / MAP2K and MAPK activation / cellular response to gamma radiation
Similarity search - Function
: / Afadin, cargo binding domain / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Ras-associating (RA) domain profile. / Ras-associating (RA) domain ...: / Afadin, cargo binding domain / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Ras-associating (RA) domain profile. / 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 / PDZ domain profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Domain present in PSD-95, Dlg, and ZO-1/2. / Ras subfamily of RAS small GTPases / Small GTPase / PDZ domain / Ras family / 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://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