[English] 日本語
Yorodumi
- PDB-8a4c: Structure of human Rep15:Rab3B complex. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8a4c
TitleStructure of human Rep15:Rab3B complex.
Components
  • Rab15 effector protein
  • Ras-related protein Rab-3B
KeywordsENDOCYTOSIS / Rab GTPase / Effector
Function / homology
Function and homology information


positive regulation of dopamine uptake involved in synaptic transmission / transferrin transport / receptor recycling / regulation of vesicle size / dopaminergic synapse / regulation of synaptic vesicle cycle / RAB geranylgeranylation / myosin V binding / regulation of exocytosis / vesicle docking involved in exocytosis ...positive regulation of dopamine uptake involved in synaptic transmission / transferrin transport / receptor recycling / regulation of vesicle size / dopaminergic synapse / regulation of synaptic vesicle cycle / RAB geranylgeranylation / myosin V binding / regulation of exocytosis / vesicle docking involved in exocytosis / antigen processing and presentation / protein secretion / protein localization to plasma membrane / recycling endosome / synaptic vesicle membrane / GDP binding / synaptic vesicle / early endosome membrane / vesicle / endosome membrane / endosome / GTPase activity / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / extracellular exosome / plasma membrane / cytoplasm
Similarity search - Function
Rab15 effector / Rab15 effector / Rab3 / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases ...Rab15 effector / Rab15 effector / Rab3 / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / 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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rab-3B / Rab15 effector protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsRai, A. / Vetter, I.R. / Goody, R.S.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)grant GO 284/10-1 Germany
CitationJournal: Nat Commun / Year: 2022
Title: Rep15 interacts with several Rab GTPases and has a distinct fold for a Rab effector.
Authors: Rai, A. / Singh, A.K. / Bleimling, N. / Posern, G. / Vetter, I.R. / Goody, R.S.
History
DepositionJun 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 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: Rab15 effector protein
B: Ras-related protein Rab-3B
C: Rab15 effector protein
D: Ras-related protein Rab-3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6498
Polymers103,5564
Non-polymers1,0934
Water68538
1
A: Rab15 effector protein
B: Ras-related protein Rab-3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3254
Polymers51,7782
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Rab15 effector protein
D: Ras-related protein Rab-3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3254
Polymers51,7782
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)188.810, 59.220, 109.020
Angle α, β, γ (deg.)90.000, 111.900, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Rab15 effector protein


Mass: 26800.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REP15 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6BDI9
#2: Protein Ras-related protein Rab-3B


Mass: 24978.064 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB3B / Production host: Escherichia coli (E. coli) / References: UniProt: P20337
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.73 Å3/Da / Density % sol: 54.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Bis-Tris pH 7.5, 0.2 M NaI and 20% (w/v) PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999961 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2017
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999961 Å / Relative weight: 1
ReflectionResolution: 2.75→47.1 Å / Num. obs: 29437 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 67.73 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rpim(I) all: 0.05485 / Rrim(I) all: 0.144 / Net I/σ(I): 14.13
Reflection shellResolution: 2.75→2.848 Å / Mean I/σ(I) obs: 1.98 / Num. unique obs: 2888 / CC1/2: 0.615 / CC star: 0.873 / Rpim(I) all: 0.6729

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8A4B

8a4b


Resolution: 2.75→47.1 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2659 1472 5 %
Rwork0.2177 27942 -
obs0.22 29414 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 167.3 Å2 / Biso mean: 77.695 Å2 / Biso min: 36.14 Å2
Refinement stepCycle: final / Resolution: 2.75→47.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5989 0 66 38 6093
Biso mean--51.62 69.94 -
Num. residues----744
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.75-2.840.40951310.381924992630100
2.84-2.940.37571340.308325272661100
2.94-3.060.32831310.268124992630100
3.06-3.20.31511340.271125442678100
3.2-3.370.33841320.241525112643100
3.37-3.580.26431340.222925282662100
3.58-3.850.25321330.210125342667100
3.85-4.240.25371340.19725482682100
4.24-4.850.23261350.167425522687100
4.85-6.110.24321340.200725592693100
6.11-47.10.24261400.21742641278199
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2686-0.202-0.67990.77950.20732.7790.0174-0.1336-0.0890.1657-0.11060.0392-0.09690.134200.4443-0.028-0.0810.46940.08380.4962-35.05730.51445.9813
20.3341-0.62260.03871.0924-0.13550.0045-1.26960.32250.1661-0.24890.36430.9488-0.21820.3853-0.00070.89980.11330.02950.7824-0.00250.7248-54.10316.979138.6589
31.5169-0.68710.1091.38761.51762.75950.3204-0.28130.60210.9276-0.35650.3683-0.8191-0.28360.00290.5965-0.0062-0.08540.4406-0.00450.5841-44.93499.384253.7358
40.4967-0.2989-0.02531.69720.22870.7537-0.4784-0.21040.71360.6330.2695-0.2315-0.57550.007100.9674-0.048-0.14990.8015-0.03470.6884-39.381410.237960.4386
52.09970.045-0.28062.46960.98210.84830.03920.29910.1359-0.2806-0.016-0.32-0.07680.345400.4148-0.01230.02210.45960.01370.3952-54.8804-14.952236.6464
60.0467-0.16020.18610.4663-0.09520.1925-0.00580.7320.24060.10510.04220.0144-0.25780.152800.7588-0.126-0.01830.7270.01970.5383-61.6882-10.899127.8395
70.84820.3755-0.1080.90080.74280.6751-0.043-0.21040.20540.2121-0.2224-0.26090.28820.372300.42790.02240.00550.4655-0.02440.5165-57.8371-9.490543.9504
80.75050.30810.44731.87720.94480.4901-0.0813-0.32070.20950.20860.0301-0.36960.11840.0555-00.5569-0.01160.06430.4422-0.0340.4649-62.9883-19.62447.9585
90.28140.0701-0.62750.0203-0.2431.3958-0.35170.19870.301-0.0081-0.0520.46110.7824-0.8385-0.1260.22910.0612-0.02760.6923-0.03210.6731-68.4826-17.446441.8918
100.11480.17380.13710.27450.17260.2339-0.0090.1718-0.0327-0.4696-0.2392-0.2171-0.1254-0.121800.6265-0.00420.15560.5940.08440.518-53.3162-34.854142.2345
110.83330.51990.31540.869-0.33050.53820.22730.2544-0.0922-0.2851-0.03660.16070.1023-0.028200.4892-0.01550.09580.4397-0.01140.5627-63.8337-29.118939.7964
120.49920.12090.11781.20450.1680.37130.45890.0581-0.2991-1.3973-0.33970.49910.0408-0.4918-0.02650.5130.081-0.1580.6188-0.00720.5618-68.291-18.126430.9685
130.0034-0.0672-0.09870.81310.5560.4133-0.2222-0.7371-0.33060.5914-0.0264-0.0674-0.66750.614-00.5186-0.0228-0.09850.97390.14670.8273-16.42045.057926.454
140.0779-0.0599-0.1080.04750.0870.1922-0.05320.0592-0.7366-1.1604-0.4164-0.48380.7517-0.31700.6737-0.0779-0.00060.60070.130.7851-34.4803-9.62238.9112
150.08170.11990.52350.07670.50181.6202-0.10520.14390.1798-0.0283-0.13230.2055-0.3116-0.059-00.5029-0.0556-0.03690.51860.06380.6133-28.03699.733524.9856
160.9882-0.5210.62220.64530.130.9376-0.2190.1050.4023-0.7072-0.048-0.5711-0.58140.815900.8696-0.09750.01650.74350.09980.8009-25.100413.375815.5344
170.40330.72760.57490.97710.3291.23790.2161-0.0902-0.22330.2827-0.2598-0.04510.0222-0.1173-00.8036-0.0260.04220.57910.03220.6205-36.07732.163617.8941
180.7229-0.39410.15920.59840.07540.09110.00440.4251-0.7391-0.8178-0.38-0.2890.07790.094800.7154-0.0532-0.03170.6978-0.10540.7156-35.74631.91719.5673
190.94560.53410.30641.09681.10171.0942-0.07110.1498-0.3758-0.41330.2248-0.36330.49810.0549-0.00050.43260.14010.00550.60620.06320.822-25.5583-4.035419.4904
200.5526-0.50810.59251.0882-1.05930.847-0.2380.0526-0.7655-0.6225-0.01270.07230.6180.296300.79350.14850.16860.736-0.02370.8623-24.132-9.431912.1141
210.05740.00780.15550.06560.03460.31910.10091.04540.49040.04220.3764-0.17540.77720.41950.01031.0134-0.18870.43161.3701-0.04011.1766-15.38998.06847.851
220.2270.2265-0.05470.19830.02660.2276-0.61780.4612-0.2440.07050.262-1.55841.24171.38360.00230.81990.05650.11240.851-0.01070.9945-18.9115-4.772711.2758
231.0531-1.10470.65542.25980.72091.90010.1922-0.1622-0.0610.411-0.08030.1046-0.1264-0.2689-00.46080.01780.02290.46-0.01350.4219-50.942619.473317.2164
240.0032-0.1016-0.01920.7977-0.09420.15820.0486-0.1981-0.1865-0.17830.2181-0.15380.11440.240100.5158-0.01640.06690.8234-0.09290.5826-39.260623.393722.905
251.322-0.96750.47870.5491-0.08260.80710.2281-0.3703-0.3319-0.0628-0.0547-0.1233-0.12720.145600.5426-0.0240.04260.4578-0.02040.5112-50.027115.496614.8976
260.0851-0.5335-0.05251.58840.1151-0.02960.37680.16440.1625-0.0247-0.135-0.3038-0.20050.130500.53510.03080.0460.4562-0.01190.4288-45.741525.70655.1895
270.47820.5718-0.68140.7338-0.50480.77760.14840.15840.0627-0.02630.0040.03520.3478-0.616-00.5748-0.0593-0.03850.5115-0.07170.4431-52.728721.19175.1247
280.3543-0.3854-0.0620.38230.01620.1175-0.141-0.55170.3140.7064-0.3161-0.6309-0.3018-0.293300.7262-0.06860.00780.61740.00610.5041-42.815540.527115.786
291.7761-0.7473-0.81231.51540.66450.54650.0297-0.04750.0653-0.0907-0.17260.4922-0.3876-0.2886-00.5749-0.0029-0.01750.5039-0.03720.5164-55.786830.314111.6185
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 114 )A18 - 114
2X-RAY DIFFRACTION2chain 'A' and (resid 115 through 143 )A115 - 143
3X-RAY DIFFRACTION3chain 'A' and (resid 144 through 190 )A144 - 190
4X-RAY DIFFRACTION4chain 'A' and (resid 191 through 236 )A191 - 236
5X-RAY DIFFRACTION5chain 'B' and (resid 18 through 56 )B18 - 56
6X-RAY DIFFRACTION6chain 'B' and (resid 57 through 69 )B57 - 69
7X-RAY DIFFRACTION7chain 'B' and (resid 70 through 91 )B70 - 91
8X-RAY DIFFRACTION8chain 'B' and (resid 92 through 123 )B92 - 123
9X-RAY DIFFRACTION9chain 'B' and (resid 124 through 135 )B124 - 135
10X-RAY DIFFRACTION10chain 'B' and (resid 136 through 146 )B136 - 146
11X-RAY DIFFRACTION11chain 'B' and (resid 147 through 171 )B147 - 171
12X-RAY DIFFRACTION12chain 'B' and (resid 172 through 187 )B172 - 187
13X-RAY DIFFRACTION13chain 'C' and (resid 18 through 37 )C18 - 37
14X-RAY DIFFRACTION14chain 'C' and (resid 38 through 51 )C38 - 51
15X-RAY DIFFRACTION15chain 'C' and (resid 52 through 89 )C52 - 89
16X-RAY DIFFRACTION16chain 'C' and (resid 90 through 103 )C90 - 103
17X-RAY DIFFRACTION17chain 'C' and (resid 104 through 143 )C104 - 143
18X-RAY DIFFRACTION18chain 'C' and (resid 144 through 155 )C144 - 155
19X-RAY DIFFRACTION19chain 'C' and (resid 156 through 174 )C156 - 174
20X-RAY DIFFRACTION20chain 'C' and (resid 175 through 214 )C175 - 214
21X-RAY DIFFRACTION21chain 'C' and (resid 215 through 224 )C215 - 224
22X-RAY DIFFRACTION22chain 'C' and (resid 225 through 235 )C225 - 235
23X-RAY DIFFRACTION23chain 'D' and (resid 18 through 44 )D18 - 44
24X-RAY DIFFRACTION24chain 'D' and (resid 45 through 56 )D45 - 56
25X-RAY DIFFRACTION25chain 'D' and (resid 57 through 91 )D57 - 91
26X-RAY DIFFRACTION26chain 'D' and (resid 92 through 122 )D92 - 122
27X-RAY DIFFRACTION27chain 'D' and (resid 123 through 135 )D123 - 135
28X-RAY DIFFRACTION28chain 'D' and (resid 136 through 146 )D136 - 146
29X-RAY DIFFRACTION29chain 'D' and (resid 147 through 187 )D147 - 187

+
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