[English] 日本語
Yorodumi
- PDB-6oq3: Crystal Structure of the Ternary Complex of KRIT1 bound to both t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6oq3
TitleCrystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and HKi2
Components
  • Krev interaction trapped protein 1
  • Ras-related protein Rap-1b
KeywordsCELL ADHESION / Complex / Small molecules / GTPase / KRIT1
Function / homology
Function and homology information


Rap protein signal transduction / GTPase regulator activity / regulation of cell junction assembly / endothelium development / modification of postsynaptic structure / positive regulation of integrin activation / negative regulation of calcium ion-dependent exocytosis / negative regulation of synaptic vesicle exocytosis / calcium-ion regulated exocytosis / integrin activation ...Rap protein signal transduction / GTPase regulator activity / regulation of cell junction assembly / endothelium development / modification of postsynaptic structure / positive regulation of integrin activation / negative regulation of calcium ion-dependent exocytosis / negative regulation of synaptic vesicle exocytosis / calcium-ion regulated exocytosis / integrin activation / Rap1 signalling / establishment of endothelial barrier / MET activates RAP1 and RAC1 / negative regulation of endothelial cell migration / regulation of establishment of cell polarity / azurophil granule membrane / small GTPase-mediated signal transduction / p130Cas linkage to MAPK signaling for integrins / negative regulation of endothelial cell proliferation / GRB2:SOS provides linkage to MAPK signaling for Integrins / regulation of angiogenesis / negative regulation of endothelial cell apoptotic process / phosphatidylinositol-4,5-bisphosphate binding / lipid droplet / Integrin signaling / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cell redox homeostasis / cellular response to cAMP / negative regulation of angiogenesis / small monomeric GTPase / establishment of localization in cell / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / 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 / cell-cell junction / GDP binding / Signaling by BRAF and RAF1 fusions / G protein activity / angiogenesis / microtubule binding / cytoskeleton / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / GTPase activity / Neutrophil degranulation / GTP binding / protein-containing complex binding / glutamatergic synapse / protein-containing complex / extracellular space / extracellular exosome / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
KRIT, N-terminal NPxY motif-rich region / Krev interaction trapped protein 1, FERM domain C-lobe / KRIT, N-terminal NPxY motif-rich domain superfamily / : / : / NUDIX, or N-terminal NPxY motif-rich, region of KRIT / KRIT1 ankyrin-repeats domain / KRIT1/FRMD8, FERM domain C-lobe / Ras-related protein Rap1 / Acyl-CoA Binding Protein - #10 ...KRIT, N-terminal NPxY motif-rich region / Krev interaction trapped protein 1, FERM domain C-lobe / KRIT, N-terminal NPxY motif-rich domain superfamily / : / : / NUDIX, or N-terminal NPxY motif-rich, region of KRIT / KRIT1 ankyrin-repeats domain / KRIT1/FRMD8, FERM domain C-lobe / Ras-related protein Rap1 / Acyl-CoA Binding Protein - #10 / Acyl-CoA Binding Protein / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / FERM central domain / PH-domain like / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Small GTPase, Ras-type / Small GTPase Ras domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Rab subfamily of small GTPases / Ankyrin repeat-containing domain superfamily / Ubiquitin-like (UB roll) / Small GTP-binding protein domain / PH-like domain superfamily / Roll / P-loop containing nucleotide triphosphate hydrolases / Roll / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2-hydroxynaphthalene-1-carbaldehyde / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Krev interaction trapped protein 1 / Ras-related protein Rap-1b
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGingras, A.R.
CitationJournal: Faseb Bioadv / Year: 2021
Title: Inhibition of the HEG1-KRIT1 interaction increases KLF4 and KLF2 expression in endothelial cells
Authors: Lopez-Ramirez, M.A. / McCurdy, S. / Li, W. / Haynes, M.K. / Hale, P. / Francisco, K. / Oukoloff, K. / Bautista, M. / Choi, C.H. / Sun, H. / Gongol, B. / Shyy, J.Y. / Ballatore, C. / Sklar, L.A. / Gingras, A.R.
History
DepositionApr 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _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.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.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
Revision 1.2Oct 11, 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: Krev interaction trapped protein 1
B: Ras-related protein Rap-1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1125
Polymers56,3932
Non-polymers7193
Water59433
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.110, 76.830, 58.210
Angle α, β, γ (deg.)90.000, 92.281, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Krev interaction trapped protein 1 / Krev interaction trapped 1 / Cerebral cavernous malformations 1 protein


Mass: 37372.348 Da / Num. of mol.: 1 / Fragment: FERM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRIT1, CCM1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O00522
#2: Protein Ras-related protein Rap-1b / GTP-binding protein smg p21B


Mass: 19020.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAP1B, OK/SW-cl.11 / Production host: Escherichia coli (E. coli) / References: UniProt: P61224

-
Non-polymers , 4 types, 36 molecules

#3: Chemical ChemComp-7WO / 2-hydroxynaphthalene-1-carbaldehyde


Mass: 172.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H8O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20-25% PEG 3,350, 100 mM Tris, pH 8.5, 100 mM KCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976484 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976484 Å / Relative weight: 1
ReflectionResolution: 1.85→46.4 Å / Num. obs: 42373 / % possible obs: 98.6 % / Redundancy: 3.78 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Net I/σ(I): 16.49
Reflection shellResolution: 1.85→1.96 Å / Rmerge(I) obs: 1.406 / Num. unique obs: 6656 / CC1/2: 0.78

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4hdo

4hdo


Resolution: 1.85→46.374 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.279 / WRfactor Rwork: 0.228 / SU B: 7.648 / SU ML: 0.202 / Average fsc free: 0.6882 / Average fsc work: 0.7082 / Cross valid method: FREE R-VALUE / ESU R: 0.185 / ESU R Free: 0.173
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2923 2119 5.001 %
Rwork0.2444 40254 -
all0.247 --
obs-42373 98.592 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 52.232 Å2
Baniso -1Baniso -2Baniso -3
1--0.026 Å20 Å2-0.073 Å2
2--0.19 Å20 Å2
3----0.158 Å2
Refinement stepCycle: LAST / Resolution: 1.85→46.374 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3835 0 46 33 3914
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0123981
X-RAY DIFFRACTIONr_angle_refined_deg1.191.6375387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7565478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.55423.412211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.14115741
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2751521
X-RAY DIFFRACTIONr_chiral_restr0.0920.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022978
X-RAY DIFFRACTIONr_nbd_refined0.2180.21833
X-RAY DIFFRACTIONr_nbtor_refined0.3140.22688
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2157
X-RAY DIFFRACTIONr_metal_ion_refined0.0570.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2510.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4460.23
X-RAY DIFFRACTIONr_mcbond_it2.4315.0771900
X-RAY DIFFRACTIONr_mcangle_it4.1657.5962370
X-RAY DIFFRACTIONr_scbond_it2.3275.3562081
X-RAY DIFFRACTIONr_scangle_it3.9027.9033013
X-RAY DIFFRACTIONr_lrange_it7.27667.8826031
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.85-1.8980.5421540.53929250.53931440.1090.12397.93260.442
1.898-1.950.5221520.48728950.48931020.320.34698.2270.363
1.95-2.0060.4661470.43727960.43829940.3410.3998.29660.329
2.006-2.0680.3931430.39827060.39828970.5710.57398.34310.313
2.068-2.1360.3611400.3626660.3628520.620.61998.38710.285
2.136-2.210.3641340.33225490.33427160.6890.7198.7850.279
2.21-2.2940.3481300.31224650.31426300.7910.898.66920.257
2.294-2.3870.3371250.28323670.28625220.8270.84498.81050.229
2.387-2.4930.3151210.27223030.27424510.8470.86998.89840.23
2.493-2.6140.3271150.27621940.27923260.8240.87599.26910.225
2.614-2.7550.3141110.27921010.28122300.8630.87799.19280.233
2.755-2.9220.3661040.2819780.28420980.8370.86799.23740.24
2.922-3.1220.344970.24918340.25419520.8690.89998.92420.228
3.122-3.3710.289920.24917480.2518560.8680.89999.13790.238
3.371-3.6910.295840.22816100.23117030.8980.92599.47150.231
3.691-4.1240.218770.18814490.1915400.9460.94999.09090.202
4.124-4.7550.209670.16212910.16513680.9520.96199.2690.185
4.755-5.8090.215580.17910910.18111570.9530.95999.30860.207
5.809-8.1510.251450.1788600.1829110.9390.95699.34140.205
8.151-46.3740.236230.1724260.1755270.9420.96185.19920.221

+
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