[English] 日本語
Yorodumi
- PDB-4cz2: Complex of human VARP-ANKRD1 with Rab32-GppCp. Selenomet derivative. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4cz2
TitleComplex of human VARP-ANKRD1 with Rab32-GppCp. Selenomet derivative.
Components
  • ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27
  • RAS-RELATED PROTEIN RAB-32
KeywordsSIGNALING PROTEIN / VARP / RAB-EFFECTOR / RAB / ENDOSOME / VESICLE TRAFFICKING / MELANOSOME BIOGENESIS
Function / homology
Function and homology information


BLOC-2 complex binding / AP-3 adaptor complex binding / negative regulation of SNARE complex assembly / AP-1 adaptor complex binding / tubular endosome / endosome to melanosome transport / melanosome assembly / phagosome maturation / mitochondria-associated endoplasmic reticulum membrane contact site / early endosome to late endosome transport ...BLOC-2 complex binding / AP-3 adaptor complex binding / negative regulation of SNARE complex assembly / AP-1 adaptor complex binding / tubular endosome / endosome to melanosome transport / melanosome assembly / phagosome maturation / mitochondria-associated endoplasmic reticulum membrane contact site / early endosome to late endosome transport / GTP-dependent protein binding / RAB geranylgeranylation / melanosome membrane / melanosome organization / positive regulation of dendrite morphogenesis / RAB GEFs exchange GTP for GDP on RABs / endocytic recycling / protein localization to membrane / antigen processing and presentation / transport vesicle / phagocytic vesicle / vesicle-mediated transport / neuron projection morphogenesis / endomembrane system / GTPase activator activity / cytoplasmic vesicle membrane / guanyl-nucleotide exchange factor activity / SNARE binding / small monomeric GTPase / mitochondrion organization / intracellular protein transport / trans-Golgi network / positive regulation of neuron projection development / small GTPase binding / phagocytic vesicle membrane / melanosome / late endosome / protein transport / mitochondrial outer membrane / early endosome / lysosome / neuron projection / intracellular membrane-bounded organelle / GTPase activity / GTP binding / endoplasmic reticulum / mitochondrion / membrane / plasma membrane / cytosol
Similarity search - Function
: / Ras-related protein Rab29/Rab38/Rab32 / VPS9 domain / VPS9 domain superfamily / Vacuolar sorting protein 9 (VPS9) domain / VPS9 domain profile. / Domain present in VPS9 / Small GTPase Rab domain profile. / Ankyrin repeat-containing domain / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases ...: / Ras-related protein Rab29/Rab38/Rab32 / VPS9 domain / VPS9 domain superfamily / Vacuolar sorting protein 9 (VPS9) domain / VPS9 domain profile. / Domain present in VPS9 / Small GTPase Rab domain profile. / Ankyrin repeat-containing domain / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Ankyrin repeat / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Rab subfamily of small GTPases / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Ras-related protein Rab-32 / Ankyrin repeat domain-containing protein 27
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 Å
AuthorsPerez-Dorado, I. / Schaefer, I.B. / McCoy, A.J. / Owen, D.J. / Evans, P.R.
CitationJournal: Dev.Cell / Year: 2014
Title: Varp is Recruited on to Endosomes by Direct Interaction with Retromer, Where Together They Function in Export to the Cell Surface.
Authors: Hesketh, G.G. / Perez-Dorado, I. / Jackson, L.P. / Wartosch, L. / Schefer, I.B. / Gray, S.R. / Mccoy, A.J. / Zeldin, O.B. / Garman, E.F. / Harbour, M.E. / Evans, P.R. / Seaman, M.N. / Luzio, J.P. / Owen, D.J.
History
DepositionApr 16, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RAS-RELATED PROTEIN RAB-32
B: RAS-RELATED PROTEIN RAB-32
C: RAS-RELATED PROTEIN RAB-32
D: ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27
E: ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27
F: ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,95012
Polymers144,3146
Non-polymers1,6376
Water2,036113
1
A: RAS-RELATED PROTEIN RAB-32
B: RAS-RELATED PROTEIN RAB-32
D: ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27
E: ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3008
Polymers96,2094
Non-polymers1,0914
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint-50 kcal/mol
Surface area35080 Å2
MethodPQS
2
C: RAS-RELATED PROTEIN RAB-32
F: ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27
hetero molecules

C: RAS-RELATED PROTEIN RAB-32
F: ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3008
Polymers96,2094
Non-polymers1,0914
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5640 Å2
ΔGint-37.1 kcal/mol
Surface area35550 Å2
MethodPQS
3
A: RAS-RELATED PROTEIN RAB-32
D: ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6504
Polymers48,1052
Non-polymers5462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-9.8 kcal/mol
Surface area19360 Å2
MethodPISA
4
B: RAS-RELATED PROTEIN RAB-32
E: ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6504
Polymers48,1052
Non-polymers5462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-7.3 kcal/mol
Surface area18970 Å2
MethodPISA
5
C: RAS-RELATED PROTEIN RAB-32
F: ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6504
Polymers48,1052
Non-polymers5462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-7.9 kcal/mol
Surface area19090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.050, 122.490, 131.580
Angle α, β, γ (deg.)90.00, 113.25, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-2004-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.2367, 0.7547, -0.6119), (0.7707, -0.5294, -0.3548), (-0.5916, -0.3875, -0.7069)19.7542, -0.566, 40.6505
3given(-0.1603, -0.7737, 0.6129), (0.6927, -0.5306, -0.4886), (0.7032, 0.3463, 0.621)-23.4001, 8.4773, -36.2571
4given(1), (1), (1)
5given(0.2563, 0.7643, -0.5918), (0.7634, -0.5356, -0.3611), (-0.5929, -0.3592, -0.7207)19.2829, -0.4206, 40.7597
6given(-0.2363, -0.7869, 0.57), (0.7501, -0.5206, -0.4078), (0.6177, 0.3312, 0.7133)-18.8901, 2.0906, -40.8071

-
Components

#1: Protein RAS-RELATED PROTEIN RAB-32 / RAB32


Mass: 25792.365 Da / Num. of mol.: 3 / Fragment: RESIDUES 450-640
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: Q13637
#2: Protein ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27 / VPS9 DOMAIN-CONTAINING PROTEIN / VPS9-DOMAIN ANKYRIN REPEAT PROTEIN


Mass: 22312.137 Da / Num. of mol.: 3
Fragment: FIRST ANKYRIN REPEAT-CONTAINING DOMAIN, RESIDUES 1-225
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: Q96NW4
#3: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsNTERMINAL SEQUENCE GPLGSM IS AN INSERTION COMING FROM THE EXPRESSION PLASMID USED. GLN 85 WAS ...NTERMINAL SEQUENCE GPLGSM IS AN INSERTION COMING FROM THE EXPRESSION PLASMID USED. GLN 85 WAS MUTATED TO LEU. VAL 100, GLN 153, VAL 158 AND ILE 192 WERE MUTATED TO MET. NTERMINAL SEQUENCE GPLGSM IS AN INSERTION COMING FROM THE EXPRESSION PLASMID USED. LAST SIX RESIDUES CORRESPONDS TO THE 6HIS-TAG

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.4 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.97→57.05 Å / Num. obs: 33062 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.22 / Net I/σ(I): 7.8
Reflection shellResolution: 2.97→3.12 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 1.9 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CYM

4cym


Resolution: 2.97→120.89 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.89 / SU B: 18.406 / SU ML: 0.308 / Cross valid method: THROUGHOUT / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. MISSING RESIDUES. RESIDUES 1-21, 149-152 AND 198-225 OF CHAIN A. RESIDUES 1-20 AND 199-225 OF CHAIN B. RESIDUES 1- 21, 149-152 AND 198-225 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. MISSING RESIDUES. RESIDUES 1-21, 149-152 AND 198-225 OF CHAIN A. RESIDUES 1-20 AND 199-225 OF CHAIN B. RESIDUES 1- 21, 149-152 AND 198-225 OF CHAIN C. RESIDUES 450-452 AND 621-640 OF CHAIN D. RESIDUES 450-452 AND 619-640 OF CHAIN E. RESIDUES 450-453 AND 619-640 OF CHAIN F. RESIDUES FROM - 5 TO 0. CTERMINAL HIS-TAGS IN CHAINS D, E AND F.
RfactorNum. reflection% reflectionSelection details
Rfree0.2322 1679 5.1 %RANDOM
Rwork0.19489 ---
obs0.1968 31378 97.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.665 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å2-2.56 Å2
2--5.62 Å20 Å2
3----1.61 Å2
Refinement stepCycle: LAST / Resolution: 2.97→120.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8037 0 99 113 8249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0198309
X-RAY DIFFRACTIONr_bond_other_d0.0050.027890
X-RAY DIFFRACTIONr_angle_refined_deg1.581.96811312
X-RAY DIFFRACTIONr_angle_other_deg1.113318119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0760.21264
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029330
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021950
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6574.0054084
X-RAY DIFFRACTIONr_mcbond_other2.6494.0044083
X-RAY DIFFRACTIONr_mcangle_it4.4395.9925091
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9314.3734225
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.9646.3756232
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.971→3.048 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 117 -
Rwork0.326 2356 -
obs--98.6 %

+
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