[English] 日本語
Yorodumi
- PDB-7opq: Rab27a fusion with Slp2a-RBDa1 effector covalent adduct with CA1 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7opq
TitleRab27a fusion with Slp2a-RBDa1 effector covalent adduct with CA1 in C188
ComponentsSynaptotagmin-like protein 2,Ras-related protein Rab-27A
KeywordsEXOCYTOSIS / GTPase / Acrylamide / Cysteine-reactive
Function / homology
Function and homology information


multivesicular body organization / cytotoxic T cell degranulation / positive regulation of constitutive secretory pathway / positive regulation of regulated secretory pathway / melanosome localization / natural killer cell degranulation / exosomal secretion / melanosome transport / Weibel-Palade body / neurexin family protein binding ...multivesicular body organization / cytotoxic T cell degranulation / positive regulation of constitutive secretory pathway / positive regulation of regulated secretory pathway / melanosome localization / natural killer cell degranulation / exosomal secretion / melanosome transport / Weibel-Palade body / neurexin family protein binding / melanocyte differentiation / exocytic vesicle / multivesicular body sorting pathway / myosin V binding / RAB geranylgeranylation / melanosome membrane / multivesicular body membrane / RAB GEFs exchange GTP for GDP on RABs / complement-dependent cytotoxicity / vesicle docking involved in exocytosis / positive regulation of reactive oxygen species biosynthetic process / synaptic vesicle transport / Insulin processing / phosphatidylserine binding / Regulation of MITF-M-dependent genes involved in pigmentation / exocytosis / positive regulation of exocytosis / antigen processing and presentation / protein secretion / photoreceptor outer segment / phosphatase binding / positive regulation of phagocytosis / vesicle-mediated transport / phosphatidylinositol-4,5-bisphosphate binding / small monomeric GTPase / G protein activity / secretory granule / intracellular protein transport / small GTPase binding / specific granule lumen / GDP binding / blood coagulation / melanosome / late endosome / lysosome / apical plasma membrane / protein domain specific binding / GTPase activity / dendrite / Neutrophil degranulation / GTP binding / positive regulation of gene expression / Golgi apparatus / extracellular exosome / extracellular region / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Synaptotagmin-like 1-5, C2B domain / Rab27a/b / Rab-binding domain / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain profile. / : / small GTPase Rab1 family profile. / Protein kinase C conserved region 2 (CalB) / C2 domain ...Synaptotagmin-like 1-5, C2B domain / Rab27a/b / Rab-binding domain / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain profile. / : / small GTPase Rab1 family profile. / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / C2 domain superfamily / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-06D / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rab-27A / Synaptotagmin-like protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsJamshidiha, M. / Tersa, M. / Lanyon-Hogg, T. / Perez-Dorado, I. / Sutherell, C.L. / De Vita, E. / Morgan, R.M.L. / Tate, E.W. / Cota, E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC29637/A20781 United Kingdom
CitationJournal: Rsc Med Chem / Year: 2022
Title: Identification of the first structurally validated covalent ligands of the small GTPase RAB27A.
Authors: Jamshidiha, M. / Lanyon-Hogg, T. / Sutherell, C.L. / Craven, G.B. / Tersa, M. / De Vita, E. / Brustur, D. / Perez-Dorado, I. / Hassan, S. / Petracca, R. / Morgan, R.M. / Sanz-Hernandez, M. / ...Authors: Jamshidiha, M. / Lanyon-Hogg, T. / Sutherell, C.L. / Craven, G.B. / Tersa, M. / De Vita, E. / Brustur, D. / Perez-Dorado, I. / Hassan, S. / Petracca, R. / Morgan, R.M. / Sanz-Hernandez, M. / Norman, J.C. / Armstrong, A. / Mann, D.J. / Cota, E. / Tate, E.W.
History
DepositionJun 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Synaptotagmin-like protein 2,Ras-related protein Rab-27A
B: Synaptotagmin-like protein 2,Ras-related protein Rab-27A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,01116
Polymers51,7142
Non-polymers2,29614
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-44 kcal/mol
Surface area18390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.710, 76.816, 117.818
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid -35 through -31 or (resid -30...
21(chain B and (resid -35 through -32 or (resid -31...
12chain D
22chain F
13chain I
23chain J
33chain K
43chain M
53chain N
63chain O

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid -35 through -31 or (resid -30...A-35 - -31
121(chain A and (resid -35 through -31 or (resid -30...A-30
131(chain A and (resid -35 through -31 or (resid -30...A-37 - 188
141(chain A and (resid -35 through -31 or (resid -30...A-37 - 188
151(chain A and (resid -35 through -31 or (resid -30...A-37 - 188
161(chain A and (resid -35 through -31 or (resid -30...A-37 - 188
211(chain B and (resid -35 through -32 or (resid -31...B-35 - -32
221(chain B and (resid -35 through -32 or (resid -31...B-31 - -30
231(chain B and (resid -35 through -32 or (resid -31...B-35 - 188
241(chain B and (resid -35 through -32 or (resid -31...B-35 - 188
251(chain B and (resid -35 through -32 or (resid -31...B-35 - 188
261(chain B and (resid -35 through -32 or (resid -31...B-35 - 188
112chain DA204
212chain FB202
113chain IA204
213chain JA205
313chain KA206
413chain MA209 - 901
513chain NB204
613chain OB205

NCS ensembles :
ID
1
2
3

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Synaptotagmin-like protein 2,Ras-related protein Rab-27A / Breast cancer-associated antigen SGA-72M / Exophilin-4 / Rab-27 / GTP-binding protein Ram


Mass: 25857.162 Da / Num. of mol.: 2 / Mutation: Q78L,C123S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYTL2, KIAA1597, SGA72M, SLP2, SLP2A, RAB27A, RAB27 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q9HCH5, UniProt: P51159, small monomeric GTPase

-
Non-polymers , 5 types, 193 molecules

#2: Chemical ChemComp-06D / 1-[(2~{S})-2-(4-methoxyphenyl)pyrrolidin-1-yl]propan-1-one


Mass: 233.306 Da / Num. of mol.: 2 / Mutation: Q78L, C123S
Source method: isolated from a genetically manipulated source
Formula: C14H19NO2 / Source: (gene. exp.) Homo sapiens (human) / Gene: RAB27A, RAB27 / Production host: Escherichia coli BL21 (bacteria) / Feature type: SUBJECT OF INVESTIGATION / References: small monomeric GTPase
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.7 Å3/Da / Density % sol: 54.42 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.15M Ammonium sulphate, 0.1M MES pH 6.0, 15% w/v PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 30, 2017
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.23→36.52 Å / Num. obs: 54026 / % possible obs: 96.86 % / Redundancy: 2 % / Biso Wilson estimate: 41.61 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.03394 / Rpim(I) all: 0.03394 / Rrim(I) all: 0.048 / Net I/σ(I): 13.67
Reflection shellResolution: 2.23→2.31 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3596 / Mean I/σ(I) obs: 2.01 / Num. unique obs: 2005 / CC1/2: 0.76 / CC star: 0.929 / Rpim(I) all: 0.3596 / Rrim(I) all: 0.5086 / % possible all: 72.64

-
Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
xia2data scaling
PDB_EXTRACT3.25data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BC1

3bc1


Resolution: 2.23→36.52 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2239 1343 4.95 %
Rwork0.177 25809 -
obs0.1794 27152 96.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.67 Å2 / Biso mean: 46.7312 Å2 / Biso min: 22.81 Å2
Refinement stepCycle: final / Resolution: 2.23→36.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3269 0 160 179 3608
Biso mean--51.7 50.94 -
Num. residues----414
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1220X-RAY DIFFRACTION11.576TORSIONAL
12B1220X-RAY DIFFRACTION11.576TORSIONAL
21A8X-RAY DIFFRACTION11.576TORSIONAL
22B8X-RAY DIFFRACTION11.576TORSIONAL
31A12X-RAY DIFFRACTION11.576TORSIONAL
32A12X-RAY DIFFRACTION11.576TORSIONAL
33A12X-RAY DIFFRACTION11.576TORSIONAL
34A12X-RAY DIFFRACTION11.576TORSIONAL
35B12X-RAY DIFFRACTION11.576TORSIONAL
36B12X-RAY DIFFRACTION11.576TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.23-2.310.2849990.25381914201373
2.31-2.40.29721370.227526122749100
2.4-2.510.2641380.215226192757100
2.51-2.640.27261350.204326322767100
2.64-2.810.23861320.194226322764100
2.81-3.030.26671410.189726372778100
3.03-3.330.23061410.176226622803100
3.33-3.810.20611360.16182575271196
3.81-4.80.18591340.142326982832100
4.8-37.260.21071500.181828282978100

+
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://pdbjlvh1.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