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- PDB-6ze9: Non-native fold of the putative VPS39 zinc finger domain -

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Basic information

Entry
Database: PDB / ID: 6ze9
TitleNon-native fold of the putative VPS39 zinc finger domain
ComponentsVam6/Vps39-like protein
KeywordsENDOCYTOSIS / Membrane trafficking / HOPS
Function / homology
Function and homology information


lysosomal HOPS complex / endocytic recycling => GO:0032456 / AP-3 adaptor complex / HOPS complex / endosomal vesicle fusion / late endosome to lysosome transport / autophagosome-lysosome fusion / endosome to lysosome transport / intracellular protein transport / autophagy ...lysosomal HOPS complex / endocytic recycling => GO:0032456 / AP-3 adaptor complex / HOPS complex / endosomal vesicle fusion / late endosome to lysosome transport / autophagosome-lysosome fusion / endosome to lysosome transport / intracellular protein transport / autophagy / late endosome / late endosome membrane / lysosomal membrane / membrane / cytoplasm
Similarity search - Function
Vacuolar sorting protein 39/Transforming growth factor beta receptor-associated domain 2 / Vacuolar sorting protein 39 domain 2 / Vacuolar sorting protein 39/Transforming growth factor beta receptor-associated domain 1 / Vam6/VPS39/TRAP1 family / Vacuolar sorting protein 39 domain 1 / Clathrin, heavy chain/VPS, 7-fold repeat / Clathrin heavy-chain (CHCR) repeat profile. / Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / Citron homology (CNH) domain / CNH domain / Citron homology (CNH) domain profile.
Similarity search - Domain/homology
Vam6/Vps39-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsButt, B.G. / Graham, S.C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust098406/Z/12/B United Kingdom
CitationJournal: Wellcome Open Res / Year: 2020
Title: Non-native fold of the putative VPS39 zinc finger domain.
Authors: Butt, B.G. / Scourfield, E.J. / Graham, S.C.
History
DepositionJun 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Derived calculations / Category: citation / struct_conn
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vam6/Vps39-like protein
B: Vam6/Vps39-like protein
C: Vam6/Vps39-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4186
Polymers15,2223
Non-polymers1963
Water181
1
A: Vam6/Vps39-like protein
C: Vam6/Vps39-like protein
hetero molecules

A: Vam6/Vps39-like protein
C: Vam6/Vps39-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5578
Polymers20,2964
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/21
Buried area6140 Å2
ΔGint-177 kcal/mol
Surface area9470 Å2
MethodPISA
2
B: Vam6/Vps39-like protein
hetero molecules

B: Vam6/Vps39-like protein
hetero molecules

B: Vam6/Vps39-like protein
hetero molecules

B: Vam6/Vps39-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5578
Polymers20,2964
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation5_556-x,y,-z+11
crystal symmetry operation6_566x,-y+1,-z+11
Buried area6700 Å2
ΔGint-163 kcal/mol
Surface area10430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.178, 104.178, 39.423
Angle α, β, γ (deg.)90, 90, 90
Int Tables number93
Space group name H-MP4222

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Components

#1: Protein/peptide Vam6/Vps39-like protein / TRAP1-like protein / hVam6p


Mass: 5073.945 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: N-terminal residues MHHHHHHM represent the hexahistidine purification tag and
Source: (gene. exp.) Homo sapiens (human) / Gene: VPS39, KIAA0770, TLP, VAM6 / Plasmid: pOPTH / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q96JC1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.51 Å3/Da / Density % sol: 64.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES pH 7.5, 200 mM ammonium acetate, 45% (v/v) 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.28096 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 6, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28096 Å / Relative weight: 1
ReflectionResolution: 2.9→46.59 Å / Num. obs: 5148 / % possible obs: 99.3 % / Redundancy: 4.1 % / Biso Wilson estimate: 92.393 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.041 / Rrim(I) all: 0.086 / Net I/σ(I): 10.1
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.178 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 247 / CC1/2: 0.602 / Rpim(I) all: 0.632 / Rrim(I) all: 1.344 / % possible all: 100

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Processing

Software
NameVersionClassification
xia20.5.902-gffa11588-dials-1.14data reduction
xia20.5.902-gffa11588-dials-1.14data scaling
CRANK22.0.229phasing
BUSTER2.10.3refinement
RefinementMethod to determine structure: MAD / Resolution: 2.9→46.59 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.902 / SU R Cruickshank DPI: 0.55 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.614 / SU Rfree Blow DPI: 0.335 / SU Rfree Cruickshank DPI: 0.328
Details: Refined using local NCS restraints plus additional restraints for the zinc atoms to enforce chemically plausible coordination.
RfactorNum. reflection% reflectionSelection details
Rfree0.2686 286 4.89 %RANDOM
Rwork0.2376 ---
obs0.2393 5139 99.1 %-
Displacement parametersBiso mean: 122.04 Å2
Baniso -1Baniso -2Baniso -3
1--14.604 Å20 Å20 Å2
2---14.604 Å20 Å2
3---29.2081 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: LAST / Resolution: 2.9→46.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms922 0 3 1 926
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.008953HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.071284HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d315SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes157HARMONIC5
X-RAY DIFFRACTIONt_it953HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion115SEMIHARMONIC5
X-RAY DIFFRACTIONt_utility_distance12HARMONIC1
X-RAY DIFFRACTIONt_utility_angle15HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact585SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.65
X-RAY DIFFRACTIONt_other_torsion19.6
LS refinement shellResolution: 2.9→2.98 Å
RfactorNum. reflection% reflection
Rfree0.3028 18 -
Rwork0.2535 --
obs0.2558 368 100 %
Refinement TLS params.

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)
116.63090.50130.76514.3013-1.86645.75260.06060.6243-0.62130.62430.0907-0.0299-0.6213-0.0299-0.15130.26950.24670.0418-0.1886-0.1582-0.060329.101533.38714.3792
216.6309-02.814616.4273-5.82083.76010.14740.5241-0.47230.52410.0260.6639-0.47230.6639-0.1734-0.27440.30140.20210.60790.0632-0.237448.114626.32345.5119
315.2652-5.25970.04131.8668-1.0621.56730.37150.46750.05630.46750.2286-0.21590.0563-0.2159-0.60010.21010.21530.00210.1387-0.1322-0.033623.735331.449915.9971
43.57790.5775-3.76824.26421.05528.19190.0338-0.7737-0.1002-0.7737-1.05460.4559-0.10020.45591.0208-0.28280.0834-0.04390.26040.25880.11065.352752.824518.1416
57.3702-4.77372.7067.4218-0.110516.6309-0.01770.434-0.91110.4340.06950.036-0.91110.036-0.0518-0.19850.16880.0530.2336-0.17950.0118-13.244760.819527.6767
66.7509-3.4058-3.44891.75762.16358.81830.2269-0.34580.1326-0.3458-0.82810.56810.13260.56810.6012-0.21560.06910.02980.17450.24320.0328.213951.978413.0254
78.9803-2.84624.3690.23662.128816.6309-0.16010.1262-1.0250.12620.48450.0569-1.0250.0569-0.32440.16880.21010.0651-0.1377-0.08920.003428.914336.156213.122
80-5.8208-5.434.11322.300216.6309-0.17030.0573-0.35750.05730.3407-0.633-0.3575-0.633-0.17030.27620.20520.13330.2459-0.0512-0.126123.834728.4933-7.8124
93.3178-4.84192.23153.7052-0.416610.98510.52640.1064-0.36110.1064-0.03050.0471-0.36110.0471-0.49590.0460.21120.11660.0665-0.06450.177329.419239.675112.11
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|-4 - A|848 }A-4 - 848
2X-RAY DIFFRACTION2{ A|849 - A|859 }A849 - 859
3X-RAY DIFFRACTION3{ A|860 - A|875 }A860 - 875
4X-RAY DIFFRACTION3{ A|1001 - A|1001 }A1001
5X-RAY DIFFRACTION4{ B|-4 - B|848 }B-4 - 848
6X-RAY DIFFRACTION5{ B|849 - B|859 }B849 - 859
7X-RAY DIFFRACTION6{ B|860 - B|875 }B860 - 875
8X-RAY DIFFRACTION6{ B|1001 - B|1001 }B1001
9X-RAY DIFFRACTION7{ C|-3 - C|848 }C-3 - 848
10X-RAY DIFFRACTION8{ C|849 - C|859 }C849 - 859
11X-RAY DIFFRACTION9{ C|860 - C|869 }C860 - 869
12X-RAY DIFFRACTION9{ C|1001 - C|1001 }C1001
13X-RAY DIFFRACTION9{ C|1002 - C|1002 }C1002

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