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- PDB-5bv0: Crystal Structure of a Complex Between the SNARE Nyv1 and the HOP... -

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Basic information

Entry
Database: PDB / ID: 5bv0
TitleCrystal Structure of a Complex Between the SNARE Nyv1 and the HOPS Vps33-Vps16 subcomplex from Chaetomium thermophilum
Components
  • SM (Sec1/Munc18-like) protein
  • SNARE domain
  • Vps16
KeywordsTRANSPORT PROTEIN / Membrane trafficking / SM protein / HOPS complex / thermophile / SNARE domain
Function / homology
Function and homology information


HOPS complex / vacuole fusion, non-autophagic / endosomal transport / ligase activity / vesicle-mediated transport / endomembrane system / intracellular protein transport / actin binding / endosome / intracellular membrane-bounded organelle ...HOPS complex / vacuole fusion, non-autophagic / endosomal transport / ligase activity / vesicle-mediated transport / endomembrane system / intracellular protein transport / actin binding / endosome / intracellular membrane-bounded organelle / membrane / cytoplasm
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 ...: / 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 / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain / Sec1-like protein / Sec1-like, domain 2 / Sec1-like superfamily / Sec1-like, domain 3a / Sec1 family / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Longin-like domain superfamily / 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
Synaptobrevin homolog YKT6 / 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: 3.1 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 5, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Database references / Category: pdbx_audit_support / struct_ref_seq_dif
Item: _pdbx_audit_support.funding_organization / _struct_ref_seq_dif.details
Revision 1.5Sep 27, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SM (Sec1/Munc18-like) protein
B: Vps16
C: SNARE domain


Theoretical massNumber of molelcules
Total (without water)104,8273
Polymers104,8273
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.030, 258.936, 75.274
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Detailsauthors have used gel filtration to support the active biological unit

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Components

#1: Protein SM (Sec1/Munc18-like) protein / VPS33


Mass: 73990.117 Da / Num. of mol.: 1
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 Vps16


Mass: 26005.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: VPS16 / Plasmid: pQLinkH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0S6M7*PLUS
#3: Protein/peptide SNARE domain / NYV1


Mass: 4830.799 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0032860 / Plasmid: pQLinkH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0S5G3
Has protein modificationN
Sequence detailsTHE SAMPLE SEQEUNCE CORRESPONDING TO CHAIN C IS THE FOLLOWING: ...THE SAMPLE SEQEUNCE CORRESPONDING TO CHAIN C IS THE FOLLOWING: GSVENNGGDSINSVQREIEDVRGIMSRNIEGLLERGERIDLLVDKTDRLGGSAREFRLRSRGLKRKM. HOWEVER, A PORTION OF THE N-TERMINAL SEGMENT COULD NOT BE MODELED BECAUSE DISORDERED. SEE SEQADV REMARK. RESIDUES 165-179 OF NYV1 (CHAIN C) EXTENSIVELY OVERLAP ON A SYMMETRY-RELATED INSTANCE OF THEMSELVES IN AN ANTIPARALLEL FASHION DUE TO 2-FOLD CRYSTALLOGRAPHIC SYMMETRY. ACCORDINGLY WE HAVE MODELED THIS SEGMENT WITH OCCUPANCY 0.5 SINCE ONE NYV1 165-179 SEGMENT IS SHARED BY TWO VPS33 MOLECULES AT A CRYSTAL CONTACT. DURING REFINEMENT WE SUPPRESS CRYSTAL CONTACT CONTRIBUTIONS FOR THIS SEGMENT. SINCE THE OVERLAPPED ELECTRON DENSITY DOES NOT ALLOW UNAMBIGUOUS ASSIGNMENT OF SIDE-CHAINS THE RESIDUES FOR 165-179 ARE LABELED UNK. THE RESIDUE NUMBERING REFLECTS OUR BEST ESTIMATE OF THE ACTUAL RESIDUES INVOLVED, HOWEVER. MORE DETAILS ARE IN THE SUPPLEMENTARY MATERIAL OF THE ASSOCIATED PAPER. THE REMAINDER OF NYV1 (183-202) IS MODELED AT FULL OCCUPANCY AND DOES NOT OVERLAP. AUTHORS HAVE INDICATED THAT THE SEQUENCES IN UNIPROT ENTRIES G0SCM5_CHATD AND G0S236_CHATD ARE NOT CORRECT

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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: 4.58 Å3/Da / Density % sol: 73.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: TRIS-HCl buffer, 0.8M Na Tartrate, 0.5% w/v PEG 5000 monomethyl ether

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2014
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 38474 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 82 Å2 / Rmerge(I) obs: 0.08 / Χ2: 0.982 / Net I/av σ(I): 23.84 / Net I/σ(I): 8.3 / Num. measured all: 276083
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.05-3.16.80.77818280.83698.2
3.1-3.1670.69519350.84799.4
3.16-3.227.20.66218700.83100
3.22-3.297.20.55319150.869100
3.29-3.367.30.46818700.857100
3.36-3.437.30.36919070.876100
3.43-3.527.30.27418740.907100
3.52-3.627.30.20619230.905100
3.62-3.727.40.18319010.911100
3.72-3.847.30.13618940.919100
3.84-3.987.30.10819140.947100
3.98-4.147.30.09119031.033100
4.14-4.337.30.08219291.143100
4.33-4.567.30.07119101.193100
4.56-4.847.20.06519441.264100
4.84-5.217.10.06219221.087100
5.21-5.7470.05719621.003100
5.74-6.576.90.05119531.013100
6.57-8.277.20.03520081.025100
8.27-506.70.02421121.15199.7

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4kmo


Resolution: 3.1→49.466 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2461 1877 5.11 %Random selection 5%
Rwork0.1948 34832 --
obs0.1974 36709 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 347.38 Å2 / Biso mean: 116.1143 Å2 / Biso min: 32.13 Å2
Refinement stepCycle: final / Resolution: 3.1→49.466 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6659 0 0 0 6659
Num. residues----846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056759
X-RAY DIFFRACTIONf_angle_d1.0659113
X-RAY DIFFRACTIONf_chiral_restr0.0441041
X-RAY DIFFRACTIONf_plane_restr0.0051184
X-RAY DIFFRACTIONf_dihedral_angle_d15.1362543
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.18380.34611430.29922616275999
3.1838-3.27750.34721580.278826292787100
3.2775-3.38320.27461470.245826242771100
3.3832-3.50410.29441240.226226652789100
3.5041-3.64440.26591420.21126432785100
3.6444-3.81020.26531370.189526632800100
3.8102-4.0110.24111140.177726662780100
4.011-4.26210.211390.171926602799100
4.2621-4.5910.24521640.163826712835100
4.591-5.05260.2191450.168227162861100
5.0526-5.78280.25111700.195126652835100
5.7828-7.2820.25461450.225627282873100
7.282-49.47190.21531490.177328863035100
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)
10.5686-0.023-0.09430.2854-0.08430.1083-0.042-0.486-0.02480.37850.16390.1860.1774-0.28190.06070.5553-0.29430.09370.55150.25550.566-12.967338.0935.4436
20.2429-0.15020.08860.057-0.03860.0440.02570.2252-0.0665-0.0919-0.0437-0.13610.19050.3355-0.00030.63450.0593-0.05210.3051-0.1130.46763.033433.5327-19.3238
30.47730.0255-0.15970.2922-0.16710.5740.01190.1431-0.1048-0.01850.0159-0.07110.09870.0365-00.39610.0409-0.02350.3589-0.01440.41276.541753.3336-11.7566
40.0071-0.0022-0.0167-0.00020.00680.0243-0.16710.0772-0.10950.0048-0.2756-0.10680.0028-0.0422-0.00030.60740.1715-0.01561.0869-0.00350.5435-3.117757.351126.4172
50.01460.0132-0.02150.07280.04590.082-0.0941-0.17460.1466-0.09140.06460.01990.27970.12790.00010.6982-0.04830.01421.22820.06470.6933-16.133361.514711.0246
60.03760.0105-0.04540.0694-0.08390.1110.1008-0.2347-0.13750.3180.1303-0.091-0.4832-0.33570.00460.45670.08070.04240.94260.07790.5765-22.643570.6458-10.8335
70.315-0.1988-0.01770.4066-0.00730.0457-0.02150.39440.4184-0.42120.11050.1096-0.3202-0.20550.08340.680.0081-0.09631.22160.13280.55-20.268963.7219-35.3577
80.033-0.0618-0.00440.11590.01280.0034-0.0717-0.03360.10040.0099-0.07570.0505-0.12560.033901.8930.32430.10791.58490.00231.63141.6368-3.0303-29.4887
90.01030.0259-0.00250.013-0.0001-0.00240.50840.13590.2615-0.19420.2315-0.0820.25220.0005-0.00051.5975-0.46390.16191.092-0.23271.32456.520928.6354-33.3294
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 215 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 216 through 411 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 412 through 659 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 524 through 534 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 535 through 605 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 606 through 657 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 658 through 730 )B0
8X-RAY DIFFRACTION8chain 'C' and (resid 165 through 178 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 179 through 202 )C0

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