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- PDB-2vx8: Vamp7 longin domain Hrb peptide complex -

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Basic information

Entry
Database: PDB / ID: 2vx8
TitleVamp7 longin domain Hrb peptide complex
ComponentsNUCLEOPORIN-LIKE PROTEIN RIP, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7
KeywordsENDOCYTOSIS / EXOCYTOSIS / MEMBRANE PROTEIN / SIGNAL-ANCHOR / SNARE / MEMBRANE / ENDOSOME / LYSOSOME / TRANSPORT / CYTOPLASMIC VESICLE / ENDOPLASMIC RETICULUM / PROTEIN TRANSPORT / VESICLE TRANSPORT / TRANSMEMBRANE / GOLGI APPARATUS / CLATHRIN ADAPTOR
Function / homology
Function and homology information


regulation of protein targeting to vacuolar membrane / neutrophil degranulation / spermatid nucleus differentiation / acrosome assembly / intermediate filament organization / eosinophil degranulation / SNARE complex / calcium-ion regulated exocytosis / vesicle fusion / positive regulation of dendrite morphogenesis ...regulation of protein targeting to vacuolar membrane / neutrophil degranulation / spermatid nucleus differentiation / acrosome assembly / intermediate filament organization / eosinophil degranulation / SNARE complex / calcium-ion regulated exocytosis / vesicle fusion / positive regulation of dendrite morphogenesis / Golgi to plasma membrane protein transport / phagocytosis, engulfment / SNARE complex assembly / endosome to lysosome transport / transport vesicle membrane / pseudopodium / endoplasmic reticulum to Golgi vesicle-mediated transport / nuclear pore / mRNA export from nucleus / transport vesicle / phagocytic vesicle / vesicle-mediated transport / GTPase activator activity / cell projection / phagocytic vesicle membrane / apical part of cell / late endosome membrane / Cargo recognition for clathrin-mediated endocytosis / lamellipodium / Clathrin-mediated endocytosis / cytoplasmic vesicle / neuron projection / lysosomal membrane / neuronal cell body / intracellular membrane-bounded organelle / synapse / endoplasmic reticulum membrane / perinuclear region of cytoplasm / cell surface / Golgi apparatus / DNA binding / RNA binding / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
: / : / Longin domain / Longin domain profile. / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf ...: / : / Longin domain / Longin domain profile. / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / Synaptobrevin signature. / ARFGAP/RecO-like zinc finger / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Longin-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Arf-GAP domain and FG repeat-containing protein 1 / Vesicle-associated membrane protein 7
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.2 Å
AuthorsEvans, P.R. / Owen, D.J. / Luzio, J.P.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: Molecular Basis for the Sorting of the Snare Vamp7 Into Endocytic Clathrin-Coated Vesicles by the Arfgap Hrb.
Authors: Pryor, P.R. / Jackson, L. / Gray, S.R. / Edeling, M.A. / Thompson, A. / Sanderson, C.M. / Evans, P.R. / Owen, D.J. / Luzio, J.P.
History
DepositionJul 1, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NUCLEOPORIN-LIKE PROTEIN RIP, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7
B: NUCLEOPORIN-LIKE PROTEIN RIP, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7
C: NUCLEOPORIN-LIKE PROTEIN RIP, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7
D: NUCLEOPORIN-LIKE PROTEIN RIP, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8307
Polymers74,7244
Non-polymers1063
Water3,063170
1
A: NUCLEOPORIN-LIKE PROTEIN RIP, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7
B: NUCLEOPORIN-LIKE PROTEIN RIP, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4334
Polymers37,3622
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-49.5 kcal/mol
Surface area15940 Å2
MethodPQS
2
A: NUCLEOPORIN-LIKE PROTEIN RIP, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7


Theoretical massNumber of molelcules
Total (without water)18,6811
Polymers18,6811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: NUCLEOPORIN-LIKE PROTEIN RIP, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7523
Polymers18,6811
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: NUCLEOPORIN-LIKE PROTEIN RIP, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7


Theoretical massNumber of molelcules
Total (without water)18,6811
Polymers18,6811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
D: NUCLEOPORIN-LIKE PROTEIN RIP, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7162
Polymers18,6811
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)105.514, 115.102, 55.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
NUCLEOPORIN-LIKE PROTEIN RIP, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7 / HRB / HIV-1 REV-BINDING PROTEIN / REV-INTERACTING PROTEIN / REV/REX ACTIVATION DOMAIN-BINDING ...HRB / HIV-1 REV-BINDING PROTEIN / REV-INTERACTING PROTEIN / REV/REX ACTIVATION DOMAIN-BINDING PROTEIN / VAMP7 / VAMP-7 / SYNAPTOBREVIN-LIKE PROTEIN 1


Mass: 18681.023 Da / Num. of mol.: 4
Fragment: HRB, RESIDUES 136-175, VAMP7 LONGIN DOMAIN, RESIDUES 1-120
Source method: isolated from a genetically manipulated source
Details: CHIMERA OF HUMAN HRB AND MOUSE VAMP7
Source: (gene. exp.) HOMO SAPIENS (human), (gene. exp.) MUS MUSCULUS (house mouse)
Plasmid: PGEX 4T-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P52594, UniProt: P70280
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 44-163 CORRESPOND TO THE LONGIN DOMAIN OF VAMP7 RESIDUES 1-42 ARE FROM HUMAN HRB ...RESIDUES 44-163 CORRESPOND TO THE LONGIN DOMAIN OF VAMP7 RESIDUES 1-42 ARE FROM HUMAN HRB (ACCESSION NUMBER NM_004504) G43 AND THE C-TERMINAL H6 (RESIDUES 163-168) ARE CLONING ARTIFACTS

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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: 2.2 Å3/Da / Density % sol: 54.6 % / Description: A SINGLE HG DERIVATIVE WAS USED
Crystal growpH: 4
Details: 20% PEG 6000, 100MM NA CITRATE PH 4.0, 0.2M LICL, FLASH COOLED IN 22%PEG, 20% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 28, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→78 Å / Num. obs: 34876 / % possible obs: 99.3 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.7
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 6.6 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0035refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.2→57.71 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.892 / SU B: 6.678 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE CRYSTALLISED CHAIN IS A FUSION PROTEIN CORRESPONDING TO RESIDUES 136-176 OF HRB LINKED BY A SINGLE GLYCINE (RESIDUE 43) TO RESIDUES 1- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE CRYSTALLISED CHAIN IS A FUSION PROTEIN CORRESPONDING TO RESIDUES 136-176 OF HRB LINKED BY A SINGLE GLYCINE (RESIDUE 43) TO RESIDUES 1-120 OF VAMP7 THE ASYMMETRIC UNIT CONTAINS 4 MOLECULES. CHAINS C AND D ARE SELF-CONTAINED. CHAINS A & B SWAP THE FIRST 40 RESIDUES OR SO, CORRESPONDING TO THE HRB FRAGMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1747 5 %RANDOM
Rwork0.22 ---
obs0.223 33094 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.75 Å2
Baniso -1Baniso -2Baniso -3
1--2.2 Å20 Å20 Å2
2---0.13 Å20 Å2
3---2.33 Å2
Refinement stepCycle: LAST / Resolution: 2.2→57.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4245 0 3 170 4418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0224338
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9961.9525877
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4415533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.7623.613191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.42615722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2771523
X-RAY DIFFRACTIONr_chiral_restr0.1550.2670
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213247
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3031.52686
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.31924318
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.16831652
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0294.51559
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.25 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.319 111
Rwork0.258 2305

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