[English] 日本語
Yorodumi
- PDB-5bv1: Crystal Structure of a Vps33-Vps16 Complex from Chaetomium thermo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bv1
TitleCrystal Structure of a Vps33-Vps16 Complex from Chaetomium thermophilum
Components
  • Putative vacuolar protein sorting-associated protein
  • VPS33
KeywordsTRANSPORT PROTEIN / Membrane trafficking / SM protein / HOPS complex / thermophile
Function / homology
Function and homology information


HOPS complex / vacuole fusion, non-autophagic / endosomal transport / ligase activity / vesicle-mediated transport / intracellular protein transport / actin binding / endosome
Similarity search - Function
Sec1/Munc18 (SM) protein, domain 3b / Vps16, C-terminal / Vps16, N-terminal / Vacuolar protein sorting-associated protein 16 / Vps16, C-terminal domain superfamily / Vps16, C-terminal region / Vps16, N-terminal region / Vacuolar protein sorting-associated protein 33, domain 3b / Sec1/Munc18 (SM) protein, domain 2 / Syntaxin Binding Protein 1; Chain A, domain 2 ...Sec1/Munc18 (SM) protein, domain 3b / Vps16, C-terminal / Vps16, N-terminal / Vacuolar protein sorting-associated protein 16 / Vps16, C-terminal domain superfamily / Vps16, C-terminal region / Vps16, N-terminal region / Vacuolar protein sorting-associated protein 33, domain 3b / Sec1/Munc18 (SM) protein, domain 2 / Syntaxin Binding Protein 1; Chain A, domain 2 / Sec1/Munc18 (SM) protein, domain 3a / Sec1/Munc18 (SM) protein, domain 1 / Sec1-like, domain 1 / Sec1-like protein / Sec1-like, domain 2 / Sec1-like superfamily / Sec1-like, domain 3a / Sec1 family / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / WD40/YVTN repeat-like-containing domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
D-MALATE / Probable vacuolar protein sorting-associated protein 16 homolog / Small conjugating protein ligase-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.902 Å
AuthorsBaker, R.W. / Jeffrey, P.D. / Hughson, F.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071574 United States
Citation
Journal: Science / Year: 2015
Title: A direct role for the Sec1/Munc18-family protein Vps33 as a template for SNARE assembly.
Authors: Baker, R.W. / Jeffrey, P.D. / Zick, M. / Phillips, B.P. / Wickner, W.T. / Hughson, F.M.
#1: Journal: Plos One / Year: 2013
Title: Crystal Structures of the Sec1/Munc18 (SM) Protein Vps33, Alone and Bound to the Homotypic Fusion and Vacuolar Protein Sorting (HOPS) Subunit Vps16*
Authors: Baker, R.W. / Jeffrey, P.D. / Hughson, F.M.
History
DepositionJun 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VPS33
B: Putative vacuolar protein sorting-associated protein
C: VPS33
D: Putative vacuolar protein sorting-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,0736
Polymers223,8054
Non-polymers2682
Water00
1
A: VPS33
B: Putative vacuolar protein sorting-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,0363
Polymers111,9022
Non-polymers1341
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-24 kcal/mol
Surface area40630 Å2
MethodPISA
2
C: VPS33
D: Putative vacuolar protein sorting-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,0363
Polymers111,9022
Non-polymers1341
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-20 kcal/mol
Surface area40910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.280, 159.902, 97.394
Angle α, β, γ (deg.)90.000, 90.210, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12chain B
22chain D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUchain AAA5 - 6577 - 659
21GLUGLUchain CCC5 - 6577 - 659
12GLYGLYchain BBB532 - 82831 - 327
22GLYGLYchain DDD532 - 82831 - 327

NCS ensembles :
ID
1
2

-
Components

#1: Protein VPS33


Mass: 73990.117 Da / Num. of mol.: 2 / Fragment: unp residues 139-806
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0057760 / Plasmid: pQLinkH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0SCM5
#2: Protein Putative vacuolar protein sorting-associated protein


Mass: 37912.211 Da / Num. of mol.: 2 / Fragment: unp residues 503-816 / Mutation: L672V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0026760 / Plasmid: pQLinkH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0S6M7
#3: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
Sequence detailsAuthors have indicated that the sequence for the UNProt entries G0S6M7_CHATD and G0SCM5_CHATD are not correct

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 60.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: HEPES buffer, 8-10% w/v PEG 5000 monomethyl ether

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2014
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.902→159.902 Å / Num. obs: 53085 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 65.34 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 16.9 / Num. measured all: 300496
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
2.902-2.9125.80.8072.1318755098
13.469-159.9025.30.024292354997.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIXrefinement
CBASSdata collection
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KMO

4kmo


Resolution: 2.902→61.592 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 30.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2759 2699 5.09 %Random selection 5%
Rwork0.2115 50335 --
obs0.2148 53034 98.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 174.73 Å2 / Biso mean: 66.5912 Å2 / Biso min: 20.98 Å2
Refinement stepCycle: final / Resolution: 2.902→61.592 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14241 0 18 0 14259
Biso mean--78.03 --
Num. residues----1797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00614485
X-RAY DIFFRACTIONf_angle_d1.05619538
X-RAY DIFFRACTIONf_chiral_restr0.042204
X-RAY DIFFRACTIONf_plane_restr0.0042549
X-RAY DIFFRACTIONf_dihedral_angle_d15.3085480
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5687X-RAY DIFFRACTION7.817TORSIONAL
12C5687X-RAY DIFFRACTION7.817TORSIONAL
21B2835X-RAY DIFFRACTION7.817TORSIONAL
22D2835X-RAY DIFFRACTION7.817TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9023-2.95510.37671260.29422677280399
2.9551-3.01190.34961440.27592604274899
3.0119-3.07340.32771200.27042684280499
3.0734-3.14020.3891390.26342637277699
3.1402-3.21330.32541230.26192648277199
3.2133-3.29360.30421490.25812635278499
3.2936-3.38270.31711420.25512643278599
3.3827-3.48220.33141460.2552637278399
3.4822-3.59460.28351510.24362636278799
3.5946-3.7230.35631490.23652640278999
3.723-3.87210.31191300.23412631276199
3.8721-4.04830.32891440.21492672281699
4.0483-4.26160.24271110.20482660277199
4.2616-4.52860.24451800.18682593277399
4.5286-4.87810.23491630.18122645280899
4.8781-5.36870.26991350.19422664279999
5.3687-6.1450.26151660.19442656282299
6.145-7.73960.23491360.18852681281799
7.7396-61.60620.20971450.16012692283798

+
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