[English] 日本語
Yorodumi
- PDB-3law: Structure of GTP-bound L129F mutant Rab7 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3law
TitleStructure of GTP-bound L129F mutant Rab7
ComponentsRas-related protein Rab-7a
KeywordsPROTON TRANSPORT / Protein - Nucleotide complex / Protein Mutant / Charcot-Marie-Tooth disease / Cytoplasmic vesicle / Disease mutation / Endosome / GTP-binding / Lipoprotein / Lysosome / Methylation / Neuropathy / Nucleotide-binding / Phosphoprotein / Prenylation / Protein transport
Function / homology
Function and homology information


lipophagy / positive regulation of viral process / phagosome acidification / protein to membrane docking / epidermal growth factor catabolic process / negative regulation of intralumenal vesicle formation / alveolar lamellar body / negative regulation of exosomal secretion / Suppression of autophagy / phagosome-lysosome fusion ...lipophagy / positive regulation of viral process / phagosome acidification / protein to membrane docking / epidermal growth factor catabolic process / negative regulation of intralumenal vesicle formation / alveolar lamellar body / negative regulation of exosomal secretion / Suppression of autophagy / phagosome-lysosome fusion / phagosome maturation / establishment of vesicle localization / retromer complex binding / endosome to plasma membrane protein transport / melanosome membrane / phagophore assembly site membrane / protein targeting to lysosome / RAB geranylgeranylation / early endosome to late endosome transport / positive regulation of exosomal secretion / RAB GEFs exchange GTP for GDP on RABs / RHOF GTPase cycle / RHOD GTPase cycle / retrograde transport, endosome to Golgi / TBC/RABGAPs / endosome to lysosome transport / RHOJ GTPase cycle / RHOQ GTPase cycle / autophagosome membrane / RHOH GTPase cycle / CDC42 GTPase cycle / autophagosome assembly / RHOG GTPase cycle / viral release from host cell / intracellular transport / RAC2 GTPase cycle / RAC3 GTPase cycle / lipid catabolic process / bone resorption / phagocytic vesicle / Prevention of phagosomal-lysosomal fusion / RAC1 GTPase cycle / MHC class II antigen presentation / lipid droplet / small monomeric GTPase / G protein activity / secretory granule membrane / mitochondrial membrane / response to bacterium / synaptic vesicle membrane / small GTPase binding / endocytosis / positive regulation of protein catabolic process / phagocytic vesicle membrane / GDP binding / late endosome / protein transport / late endosome membrane / lysosome / endosome membrane / lysosomal membrane / GTPase activity / Neutrophil degranulation / GTP binding / Golgi apparatus / mitochondrion / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
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 nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase ...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 nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rab-7a
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMcCray, B.A. / Skordalakes, E. / Taylor, J.P.
CitationJournal: Hum.Mol.Genet. / Year: 2010
Title: Disease mutations in Rab7 result in unregulated nucleotide exchange and inappropriate activation.
Authors: McCray, B.A. / Skordalakes, E. / Taylor, J.P.
History
DepositionJan 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ras-related protein Rab-7a
B: Ras-related protein Rab-7a
C: Ras-related protein Rab-7a
D: Ras-related protein Rab-7a
E: Ras-related protein Rab-7a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,48615
Polymers117,7545
Non-polymers2,73310
Water75742
1
A: Ras-related protein Rab-7a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0973
Polymers23,5511
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ras-related protein Rab-7a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0973
Polymers23,5511
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ras-related protein Rab-7a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0973
Polymers23,5511
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ras-related protein Rab-7a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0973
Polymers23,5511
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Ras-related protein Rab-7a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0973
Polymers23,5511
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.554, 89.335, 89.378
Angle α, β, γ (deg.)71.24, 85.97, 85.91
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Ras-related protein Rab-7a


Mass: 23550.734 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB7A, RAB7 / Production host: Escherichia coli (E. coli) / References: UniProt: P51149
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.27 Å3/Da / Density % sol: 45.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.2 M sodium formate, 10mM trimethylamine hydrochloride, and 20% polyethylene glycol 3,350, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 24170 / Num. obs: 23869 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2 % / Rsym value: 0.1 / Net I/σ(I): 7.7
Reflection shellResolution: 2.8→2.871 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.417 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→19.88 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.838 / SU B: 35.857 / SU ML: 0.364 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.452 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27265 1277 5.1 %RANDOM
Rwork0.22036 ---
obs0.23678 23869 98.7 %-
all-24300 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.888 Å2
Baniso -1Baniso -2Baniso -3
1--2.02 Å20.35 Å20.09 Å2
2--0.75 Å2-1.21 Å2
3---1.98 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7044 0 165 42 7251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227349
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.9689982
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6365875
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.85324.958357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.314151264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4121540
X-RAY DIFFRACTIONr_chiral_restr0.0810.21106
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025498
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2450.23431
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3210.25010
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2289
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0880.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2950.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7221.54469
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.26927090
X-RAY DIFFRACTIONr_scbond_it1.46633305
X-RAY DIFFRACTIONr_scangle_it2.4234.52892
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 91 -
Rwork0.309 1710 -
obs--98.2 %
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)
12.4007-0.17570.66574.84461.05351.75490.01090.0259-0.0788-0.05720.0604-0.25320.04660.154-0.0713-0.09330.00750.0058-0.0281-0.0181-0.094716.355112.188732.0531
22.6658-1.0072-0.08812.65730.693.3959-0.0544-0.07190.24160.0030.0581-0.1401-0.06630.0817-0.0037-0.084-0.01760.0134-0.1065-0.0028-0.019823.6769-11.84778.6827
32.04860.90610.52332.9725-1.84743.3491-0.06560.1387-0.07980.0933-0.0845-0.25990.00890.11580.1501-0.07410.0260.0201-0.0763-0.0341-0.03529.216941.902315.9532
42.79720.4189-0.92812.3522-0.68422.11740.0391-0.3263-0.0797-0.0315-0.0884-0.0246-0.01730.24560.0493-0.035-0.0032-0.00210.017-0.0078-0.12230.74922.7593-21.6196
52.75461.2824-0.22253.36671.65864.05370.02780.1002-0.2089-0.00070.0469-0.2287-0.11270.3126-0.0748-0.07580.0037-0.0414-0.06830.0282-0.04212.29636.1486-17.4153
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 180
2X-RAY DIFFRACTION2B8 - 180
3X-RAY DIFFRACTION3C8 - 180
4X-RAY DIFFRACTION4D8 - 180
5X-RAY DIFFRACTION5E8 - 180

+
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