[English] 日本語
Yorodumi
- PDB-6djq: Vps1 GTPase-BSE fusion complexed with GDP.AlF4- -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6djq
TitleVps1 GTPase-BSE fusion complexed with GDP.AlF4-
ComponentsVps1 GTPase-BSE
KeywordsHYDROLASE / Vps1 / vacuolar protein sorting 1 / GDP.AlF4- / dynamin-related protein / DRP / dynamin / vacuole / endosome / transition state
Function / homology
Function and homology information


peroxisome fission / vacuole organization / mitochondrial fission / intracellular distribution of mitochondria / endocytosis / peroxisome / microtubule binding / microtubule / GTPase activity / GTP binding ...peroxisome fission / vacuole organization / mitochondrial fission / intracellular distribution of mitochondria / endocytosis / peroxisome / microtubule binding / microtubule / GTPase activity / GTP binding / metal ion binding / membrane
Similarity search - Function
Dynamin GTPase effector / Dynamin GTPase effector domain / Dynamin GTPase effector domain / Dynamin stalk domain / Dynamin central region / GTPase effector domain / GED domain profile. / Dynamin, GTPase domain / Dynamin, GTPase / Dynamin ...Dynamin GTPase effector / Dynamin GTPase effector domain / Dynamin GTPase effector domain / Dynamin stalk domain / Dynamin central region / GTPase effector domain / GED domain profile. / Dynamin, GTPase domain / Dynamin, GTPase / Dynamin / Dynamin-type guanine nucleotide-binding (G) domain / Dynamin-type guanine nucleotide-binding (G) domain profile. / Dynamin, N-terminal / Dynamin family / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / Vacuolar protein sorting-associated protein 1
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsVarlakhanova, N.V. / Brady, T.M. / Tornabene, B.A. / Hosford, C.J. / Chappie, J.S. / Ford, M.G.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM120102 United States
CitationJournal: J Cell Biol / Year: 2018
Title: Structures of the fungal dynamin-related protein Vps1 reveal a unique, open helical architecture.
Authors: Natalia V Varlakhanova / Frances J D Alvarez / Tyler M Brady / Bryan A Tornabene / Christopher J Hosford / Joshua S Chappie / Peijun Zhang / Marijn G J Ford /
Abstract: Dynamin-related proteins (DRPs) are large multidomain GTPases required for diverse membrane-remodeling events. DRPs self-assemble into helical structures, but how these structures are tailored to ...Dynamin-related proteins (DRPs) are large multidomain GTPases required for diverse membrane-remodeling events. DRPs self-assemble into helical structures, but how these structures are tailored to their cellular targets remains unclear. We demonstrate that the fungal DRP Vps1 primarily localizes to and functions at the endosomal compartment. We present crystal structures of a Vps1 GTPase-bundle signaling element (BSE) fusion in different nucleotide states to capture GTP hydrolysis intermediates and concomitant conformational changes. Using cryoEM, we determined the structure of full-length GMPPCP-bound Vps1. The Vps1 helix is more open and flexible than that of dynamin. This is due to further opening of the BSEs away from the GTPase domains. A novel interface between adjacent GTPase domains forms in Vps1 instead of the contacts between the BSE and adjacent stalks and GTPase domains as seen in dynamin. Disruption of this interface abolishes Vps1 function in vivo. Hence, Vps1 exhibits a unique helical architecture, highlighting structural flexibilities of DRP self-assembly.
History
DepositionMay 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Vps1 GTPase-BSE
B: Vps1 GTPase-BSE
C: Vps1 GTPase-BSE
D: Vps1 GTPase-BSE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,38220
Polymers172,0084
Non-polymers2,37416
Water34219
1
A: Vps1 GTPase-BSE
B: Vps1 GTPase-BSE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,19110
Polymers86,0042
Non-polymers1,1878
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-68 kcal/mol
Surface area29810 Å2
MethodPISA
2
C: Vps1 GTPase-BSE
D: Vps1 GTPase-BSE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,19110
Polymers86,0042
Non-polymers1,1878
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-70 kcal/mol
Surface area28910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.060, 121.220, 104.560
Angle α, β, γ (deg.)90.00, 90.60, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Vps1 GTPase-BSE


Mass: 43002.074 Da / Num. of mol.: 4 / Fragment: UNP residues 1-354, 669-698
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0061810 / Plasmid: pET15b / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: G0SFF0

-
Non-polymers , 5 types, 35 molecules

#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical
ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: AlF4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.55 Å3/Da / Density % sol: 51.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 5-10% PEG8000, 20% glycerol, 0.08 M MES, pH 5.6-6.2
PH range: 5.6-6.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.96922 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 4, 2017 / Details: Si 111
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96922 Å / Relative weight: 1
ReflectionResolution: 3.1→40.41 Å / Num. obs: 26055 / % possible obs: 84.4 % / Redundancy: 2 % / Biso Wilson estimate: 52.671 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.091 / Rrim(I) all: 0.134 / Net I/σ(I): 8.2
Reflection shellResolution: 3.1→3.29 Å / Redundancy: 2 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 2 / Num. unique obs: 3987 / CC1/2: 0.516 / Rpim(I) all: 0.474 / Rrim(I) all: 0.411 / % possible all: 79.9

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MOSFLM7.2.1data reduction
Aimless0.5.14data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3ZYC

3zyc


Resolution: 3.1→39.595 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 30.21
RfactorNum. reflection% reflectionSelection details
Rfree0.2785 1271 4.88 %Random selection
Rwork0.2223 ---
obs0.225 26023 83.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→39.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9916 0 140 19 10075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310214
X-RAY DIFFRACTIONf_angle_d0.59113964
X-RAY DIFFRACTIONf_dihedral_angle_d11.2226253
X-RAY DIFFRACTIONf_chiral_restr0.0431699
X-RAY DIFFRACTIONf_plane_restr0.0041866
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1001-3.22420.35121010.30132632X-RAY DIFFRACTION79
3.2242-3.37080.36551200.2762620X-RAY DIFFRACTION79
3.3708-3.54840.32771490.27662633X-RAY DIFFRACTION80
3.5484-3.77060.32821490.25022640X-RAY DIFFRACTION80
3.7706-4.06150.30081470.20852688X-RAY DIFFRACTION81
4.0615-4.46970.24631260.19122847X-RAY DIFFRACTION86
4.4697-5.11530.22791790.17392884X-RAY DIFFRACTION88
5.1153-6.44020.27391720.22662916X-RAY DIFFRACTION88
6.4402-39.59780.24451280.21412892X-RAY DIFFRACTION85
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)
10.11450.07320.14080.0440.08790.1743-0.17740.0056-0.0656-0.28230.0855-0.1484-0.2233-0.2167-0.03040.76440.06130.04110.37150.16250.3858.926131.476933.5513
20.0852-0.0015-0.05150.13830.05720.1998-0.05040.1058-0.0659-0.0469-0.06890.0288-0.205-0.1456-0.17120.14630.0383-0.03830.1234-0.00920.26723.2219.070747.8434
30.1232-0.0335-0.07370.16110.12640.111-0.01040.2156-0.0252-0.2027-0.11510.16420.0011-0.2413-0.230.22620.0035-0.08410.27060.0070.2589-1.254112.471840.5597
40.0751-0.0999-0.06640.15890.04190.1740.0422-0.08850.014-0.00180.0734-0.05070.05320.10770.2930.08750.0704-0.0410.16840.08980.32426.9358.682162.1402
50.034-0.0382-0.00560.0415-0.01980.0311-0.1241-0.1571-0.071-0.10250.1745-0.2288-0.23250.09880.00020.3657-0.0446-0.05670.3371-0.07670.300910.630823.857861.4978
60.1818-0.0947-0.07510.2154-0.04230.16890.0730.1062-0.0123-0.0207-0.09320.0066-0.1992-0.2016-0.16950.28670.1382-0.11790.05930.03830.4825-3.177829.559761.5642
70.00670.0294-0.01770.1281-0.09120.06350.16460.09060.00050.0407-0.03510.0964-0.148-0.10550.12590.5380.2495-0.00060.33650.02920.5301-8.448237.556756.8179
80.2281-0.07250.27670.0294-0.06170.4402-0.04240.0206-0.1553-0.06780.19380.1993-0.09840.02320.12690.6597-0.01560.16090.20410.01240.3129.41833.880746.3755
90.0841-0.0873-0.02870.07780.03410.02360.2360.1342-0.0691-0.073-0.0117-0.03420.0869-0.00640.04660.6819-0.17990.18050.64870.01340.300331.245235.49126.799
100.2271-0.2021-0.06150.36950.2370.19360.09650.1051-0.0122-0.0533-0.1057-0.2086-0.00870.0769-0.08270.59350.08110.30530.1203-0.00740.662424.169536.75320.8977
110.009-0.01160.00380.01630.00620.00730.0293-0.02850.13380.04180.00280.0216-0.0139-0.0619-0.00011.06160.12730.24130.6359-0.02860.5416-13.888412.233104.0714
120.0040.013-0.00880.0321-0.02580.0308-0.0115-0.0411-0.06540.08440.0531-0.0832-0.051-0.04440.07220.15340.2306-0.01070.46670.10150.391-3.610517.511788.9274
130.19360.18810.12380.20790.19630.3344-0.02210.00460.16350.22530.22720.0003-0.31220.09330.24390.65960.2672-0.07830.3495-0.10240.2485-0.578727.180797.5656
140.2744-0.14170.12910.5039-0.39230.2981-0.4963-0.42450.21970.10030.0749-0.0798-0.05910.0952-0.07240.85350.01270.00430.5367-0.14140.39432.312126.705295.2482
150.18270.07270.24050.05590.07980.3164-0.10810.11410.0520.13050.02050.14750.00720.27970.01260.30880.1422-0.07110.3527-0.03820.43311.456619.752580.011
160.04090.0177-0.09610.12840.03490.3286-0.1562-0.1172-0.18520.11660.07310.14040.2691-0.1153-0.13450.1340.06440.110.19750.02780.3193-5.311611.745977.537
170.09180.037-0.14530.017-0.06520.2293-0.1482-0.15950.0197-0.0918-0.03960.0280.0129-0.2138-0.14390.44940.21430.06180.3318-0.07430.5547-11.287619.144380.0713
180.0519-0.00240.10980.21680.21550.46350.19270.03750.1115-0.1213-0.009-0.0924-0.1658-0.19330.39660.09990.04340.0520.34250.08170.1921-17.51913.131286.8636
190.0315-0.0305-0.03770.01810.02540.030.189-0.01520.0364-0.0370.0662-0.1620.0687-0.0372-0.00010.4613-0.0843-0.06240.4950.13340.4516-7.0029-6.8896124.6736
200.28750.1974-0.02670.4463-0.17010.0832-0.083-0.07310.1343-0.09540.19110.22270.02990.13620.00950.92620.1374-0.08590.7318-0.03950.307619.432-10.9136-19.3892
21-0.0010.0691-0.0160.5123-0.45220.89980.15110.3037-0.097-0.0046-0.2582-0.114-0.3530.4871-0.15960.46320.11870.07910.49960.00850.198429.44012.4206-6.7492
220.7524-0.41870.04240.4738-0.04070.31380.16110.3756-0.2669-0.3626-0.00610.18710.04510.08040.54350.34170.16750.07770.34210.02350.134626.3343-1.29895.6785
230.0436-0.02540.00610.090.0124-0.0052-0.0092-0.07720.1506-0.0504-0.09920.06460.0638-0.0131-0.050.55060.0425-0.05110.3484-0.10060.21036.9506-12.4394-27.2949
240.03160.0366-0.01480.0494-0.02590.01690.05080.01850.0970.0077-0.0784-0.08140.00550.1038-0.02820.08870.0179-0.03480.5789-0.07410.588134.18810.226854.8351
250.3316-0.0102-0.02060.0921-0.05310.02930.1242-0.06750.1622-0.148-0.0946-0.24310.14530.0088-0.04270.24820.02030.05180.21110.05980.34724.840213.634445.3693
260.1824-0.0899-0.11710.19620.07960.11260.14490.098-0.0771-0.024-0.17030.04340.08270.223-0.00020.33690.0385-0.030.32440.05140.279318.1831-0.428140.5367
270.30470.0904-0.03760.02880.00630.06480.0743-0.15650.052-0.17570.06010.14770.015-0.21690.0580.38740.0796-0.07270.53840.10330.216226.6613.110828.1982
280.1641-0.2088-0.03520.28920.11260.31940.0442-0.19290.2198-0.03790.1909-0.0860.03470.52320.57790.02530.0730.03210.6070.1360.495739.0130.20829.4515
290.0927-0.06220.10630.0493-0.06890.1228-0.04450.00070.34750.2095-0.20860.1732-0.18630.0748-0.37890.4394-0.40460.10690.6564-0.19370.465333.349622.748856.2921
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 34 )
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 87 )
3X-RAY DIFFRACTION3chain 'A' and (resid 88 through 170 )
4X-RAY DIFFRACTION4chain 'A' and (resid 171 through 198 )
5X-RAY DIFFRACTION5chain 'A' and (resid 199 through 233 )
6X-RAY DIFFRACTION6chain 'A' and (resid 234 through 281 )
7X-RAY DIFFRACTION7chain 'A' and (resid 282 through 307 )
8X-RAY DIFFRACTION8chain 'A' and (resid 308 through 326 )
9X-RAY DIFFRACTION9chain 'A' and (resid 327 through 675 )
10X-RAY DIFFRACTION10chain 'A' and (resid 676 through 696 )
11X-RAY DIFFRACTION11chain 'B' and (resid 10 through 29 )
12X-RAY DIFFRACTION12chain 'B' and (resid 30 through 64 )
13X-RAY DIFFRACTION13chain 'B' and (resid 65 through 127 )
14X-RAY DIFFRACTION14chain 'B' and (resid 128 through 170 )
15X-RAY DIFFRACTION15chain 'B' and (resid 171 through 198 )
16X-RAY DIFFRACTION16chain 'B' and (resid 199 through 254 )
17X-RAY DIFFRACTION17chain 'B' and (resid 255 through 281 )
18X-RAY DIFFRACTION18chain 'B' and (resid 282 through 327 )
19X-RAY DIFFRACTION19chain 'B' and (resid 328 through 695 )
20X-RAY DIFFRACTION20chain 'C' and (resid 12 through 35 )
21X-RAY DIFFRACTION21chain 'C' and (resid 36 through 127 )
22X-RAY DIFFRACTION22chain 'C' and (resid 128 through 307 )
23X-RAY DIFFRACTION23chain 'C' and (resid 308 through 697 )
24X-RAY DIFFRACTION24chain 'D' and (resid 10 through 32 )
25X-RAY DIFFRACTION25chain 'D' and (resid 33 through 55 )
26X-RAY DIFFRACTION26chain 'D' and (resid 56 through 198 )
27X-RAY DIFFRACTION27chain 'D' and (resid 199 through 233 )
28X-RAY DIFFRACTION28chain 'D' and (resid 234 through 307 )
29X-RAY DIFFRACTION29chain 'D' and (resid 308 through 691 )

+
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