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- PDB-6def: Vps1 GTPase-BSE fusion complexed with GMPPCP -

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Basic information

Entry
Database: PDB / ID: 6def
TitleVps1 GTPase-BSE fusion complexed with GMPPCP
ComponentsVps1 GTPase-BSE
KeywordsHYDROLASE / Vps1 / Vacuolar Protein Sorting 1 / Dynamin-Related Protein / DRP / GTPase / GMPPCP / Endosome / Vacuole
Function / homology
Function and homology information


organelle organization / GTPase activity / GTP binding
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
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Putative sorting protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsFord, M.G.J. / Varlakhanova, N.V. / Brady, T.M. / Chappie, J.S. / Hosford, C.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 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)174,19012
Polymers172,0084
Non-polymers2,1828
Water8,629479
1
A: Vps1 GTPase-BSE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5483
Polymers43,0021
Non-polymers5462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Vps1 GTPase-BSE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5483
Polymers43,0021
Non-polymers5462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Vps1 GTPase-BSE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5483
Polymers43,0021
Non-polymers5462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Vps1 GTPase-BSE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5483
Polymers43,0021
Non-polymers5462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.659, 118.740, 84.140
Angle α, β, γ (deg.)90.00, 99.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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, Hydrolases
#2: Chemical
ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


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


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 14% PEG4000, 0.2 M sodium acetate, 0.1 M Tris-Cl, pH 8.7-9.0
PH range: 8.7-9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 29, 2018
Details: Si 111. Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→40.79 Å / Num. obs: 69139 / % possible obs: 92.4 % / Redundancy: 3.6 % / Biso Wilson estimate: 28.9 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.042 / Rrim(I) all: 0.08 / Net I/σ(I): 10.6
Reflection shellResolution: 2.26→2.31 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4347 / CC1/2: 0.86 / Rpim(I) all: 0.316 / Rrim(I) all: 0.59 / % possible all: 90.5

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3ZYC

3zyc


Resolution: 2.26→40.786 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2253 3324 4.81 %Random
Rwork0.1931 ---
obs0.1947 69069 92.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.26→40.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10997 0 132 479 11608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211326
X-RAY DIFFRACTIONf_angle_d0.52715409
X-RAY DIFFRACTIONf_dihedral_angle_d11.6967045
X-RAY DIFFRACTIONf_chiral_restr0.0431822
X-RAY DIFFRACTIONf_plane_restr0.0032065
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.29230.30931460.26462686X-RAY DIFFRACTION91
2.2923-2.32650.30341270.25582596X-RAY DIFFRACTION88
2.3265-2.36290.27691090.24612280X-RAY DIFFRACTION77
2.3629-2.40160.30781150.24862449X-RAY DIFFRACTION82
2.4016-2.4430.32741550.24072763X-RAY DIFFRACTION94
2.443-2.48740.28411430.23162877X-RAY DIFFRACTION97
2.4874-2.53520.27291030.22552867X-RAY DIFFRACTION96
2.5352-2.5870.28281570.21942905X-RAY DIFFRACTION97
2.587-2.64320.25741420.2232870X-RAY DIFFRACTION97
2.6432-2.70470.26041410.22182842X-RAY DIFFRACTION96
2.7047-2.77230.30551340.22842886X-RAY DIFFRACTION97
2.7723-2.84730.26641500.23792833X-RAY DIFFRACTION96
2.8473-2.9310.27951530.23012837X-RAY DIFFRACTION96
2.931-3.02560.28561730.22652814X-RAY DIFFRACTION95
3.0256-3.13370.27721290.22152738X-RAY DIFFRACTION93
3.1337-3.25910.25811390.21872666X-RAY DIFFRACTION90
3.2591-3.40740.25811100.21352298X-RAY DIFFRACTION77
3.4074-3.58690.22081390.20232552X-RAY DIFFRACTION86
3.5869-3.81150.19281380.17742944X-RAY DIFFRACTION98
3.8115-4.10550.2121330.15832901X-RAY DIFFRACTION97
4.1055-4.51820.18451290.14482921X-RAY DIFFRACTION97
4.5182-5.17090.1611560.13772847X-RAY DIFFRACTION95
5.1709-6.51050.19931260.17672569X-RAY DIFFRACTION86
6.5105-40.79290.15681770.17072804X-RAY DIFFRACTION93
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)
15.20970.67930.00833.5908-0.29722.41540.06050.0416-0.38670.62820.4162-0.38160.26570.6023-0.63620.3918-0.0608-0.00860.637-0.10920.459634.74775.276978.3743
24.28040.70540.52051.35340.05961.9740.0726-0.6748-0.35230.30640.0893-0.22150.090.0272-0.16180.33110.029-0.02760.42770.03040.302414.5615-6.664976.7481
32.35190.92510.50261.7543-0.45443.7774-0.02910.0873-0.0984-0.1390.1658-0.2339-0.18220.1897-0.09760.2321-0.0174-0.0210.2755-0.0440.358216.24171.50557.2187
47.32157.88097.84717.86598.14777.6232-0.7859-0.16650.8367-0.6292-0.23860.7243-1.1341-0.14170.77110.6402-0.0973-0.15270.5779-0.04060.633834.003218.94780.1214
57.94946.10165.53148.37175.26964.22250.06540.4424-0.5180.15470.1428-0.30920.2510.9715-0.13410.364-0.12290.05630.6014-0.0710.58147.760923.14796.0419
63.92561.29840.64792.01540.79640.5645-0.04790.3182-0.0321-0.2130.0799-0.0948-0.06430.0135-0.00050.37930.0251-0.02540.26260.04860.2341-17.9261-3.085637.4715
74.44581.51613.5646.34560.79058.4869-0.10450.66380.0212-0.71320.3368-0.341-0.2950.3329-0.21660.44060.00970.06550.3640.08630.2258-11.62716.868826.6371
84.19253.4683.42695.33073.66954.7609-0.12150.37720.2322-0.41290.11820.0913-0.5791-0.11840.1130.40120.07590.00550.25550.0670.3217-14.35085.916837.0888
98.45774.25971.49964.69952.20873.84530.0574-0.33050.605-0.0387-0.0612-0.1497-0.4525-0.09590.00590.42920.0587-0.00310.2280.00770.3836-7.162511.298753.7228
106.2075-1.3179-1.32852.98551.35282.2877-0.1166-0.4933-0.30340.2460.1552-0.05220.0887-0.0583-0.03450.3091-0.005-0.01030.23520.04990.2305-7.5201-7.310754.3098
114.7158-0.8618-1.34253.81320.9525.05880.05760.1261-0.58070.3587-0.04-0.2921-0.03680.0459-0.08220.2532-0.0115-0.05450.1342-0.03620.2966-2.4993-9.406145.1556
126.64950.3840.81381.42040.03260.82260.069-0.0966-0.2049-0.18270.05650.13030.0174-0.1054-0.1260.3384-0.0224-0.03240.22470.010.2354-22.7847-15.251541.0515
137.5911-1.3562.79373.3870.52073.19530.23130.66610.0779-1.4235-0.44580.9877-0.0081-0.23480.20490.8369-0.087-0.21420.465-0.04530.8457-52.1718-11.169127.7121
140.5233-0.05031.5172.1096-1.3927.9264-0.02240.0839-0.0969-0.38450.01290.1788-0.2062-0.35340.01650.37440.0083-0.0910.447-0.08530.357316.649825.76716.3619
153.2558-0.73741.30672.3898-0.98343.2940.21610.0499-0.3741-0.34150.00670.48080.4284-0.563-0.20420.4038-0.1093-0.11680.4685-0.08760.423813.332714.121614.8882
164.849-2.2745-2.49239.06350.42086.3705-0.02060.3921-0.4939-0.7347-0.2879-0.31920.05740.45370.29840.2257-0.0302-0.00140.41090.01030.372733.975621.599914.8432
171.8930.17951.05972.33130.09554.6514-0.20130.01950.34360.04810.0251-0.0023-0.7405-0.18070.10990.31620.0207-0.06780.29010.00640.338825.095734.454224.4007
18-0.4658-0.30090.6124-0.1034-0.85632.6959-0.16260.10.0333-0.1587-0.22190.12530.36170.91980.4070.5076-0.0211-0.08530.63090.07960.395623.298731.0147-12.555
194.26530.76674.24133.5488-0.84167.3845-0.0878-0.52620.2680.0329-0.02980.25950.3974-1.18040.00150.62120.00230.01560.4188-0.04710.468813.292632.3169-32.2602
200.5146-0.97210.23443.1845-2.2843.7904-0.2244-0.19180.09450.39970.1472-0.1991-0.23270.07250.14130.23550.0091-0.06490.3527-0.06250.359548.983116.258451.8824
213.48930.382-0.64132.04351.03198.3718-0.0624-0.41570.31540.4029-0.0127-0.4476-0.60530.01970.14460.3555-0.0281-0.16640.3279-0.09950.609458.658429.342350.0855
220.47380.05380.04681.9202-0.99174.3913-0.0149-0.07390.09170.36740.1844-0.5377-0.35990.177-0.17640.2598-0.0091-0.1020.3568-0.09560.485554.386320.088544.8759
234.32230.2505-0.01395.5821-4.65824.105-0.10730.4991-0.16870.03540.1512-0.06660.2021-0.1977-0.0360.2286-0.0133-0.00120.3317-0.10490.400947.751615.837427.8316
241.9379-0.9007-0.20644.5260.28662.2941-0.09570.0144-0.05270.13670.1531-0.03880.12-0.184-0.07040.1463-0.0305-0.01950.2687-0.0190.237833.614616.333240.809
255.238-3.3273.30574.8506-3.45793.98570.0051-0.3721-0.92570.3950.14720.6319-0.0639-0.133-0.13880.3629-0.01860.08110.3775-0.01720.358939.460710.103459.4772
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 35 )
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 198 )
3X-RAY DIFFRACTION3chain 'A' and (resid 199 through 307 )
4X-RAY DIFFRACTION4chain 'A' and (resid 308 through 348 )
5X-RAY DIFFRACTION5chain 'A' and (resid 349 through 697 )
6X-RAY DIFFRACTION6chain 'B' and (resid 9 through 87 )
7X-RAY DIFFRACTION7chain 'B' and (resid 88 through 143 )
8X-RAY DIFFRACTION8chain 'B' and (resid 144 through 170 )
9X-RAY DIFFRACTION9chain 'B' and (resid 171 through 198 )
10X-RAY DIFFRACTION10chain 'B' and (resid 199 through 254 )
11X-RAY DIFFRACTION11chain 'B' and (resid 255 through 281 )
12X-RAY DIFFRACTION12chain 'B' and (resid 282 through 347 )
13X-RAY DIFFRACTION13chain 'B' and (resid 348 through 697 )
14X-RAY DIFFRACTION14chain 'C' and (resid 10 through 74 )
15X-RAY DIFFRACTION15chain 'C' and (resid 75 through 198 )
16X-RAY DIFFRACTION16chain 'C' and (resid 199 through 233 )
17X-RAY DIFFRACTION17chain 'C' and (resid 234 through 307 )
18X-RAY DIFFRACTION18chain 'C' and (resid 308 through 348 )
19X-RAY DIFFRACTION19chain 'C' and (resid 349 through 697 )
20X-RAY DIFFRACTION20chain 'D' and (resid 9 through 87 )
21X-RAY DIFFRACTION21chain 'D' and (resid 88 through 143 )
22X-RAY DIFFRACTION22chain 'D' and (resid 144 through 170 )
23X-RAY DIFFRACTION23chain 'D' and (resid 171 through 198 )
24X-RAY DIFFRACTION24chain 'D' and (resid 199 through 281 )
25X-RAY DIFFRACTION25chain 'D' and (resid 282 through 695 )

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