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- PDB-2j9w: Structural insight into the ESCRT-I-II link and its role in MVB t... -

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Basic information

Entry
Database: PDB / ID: 2j9w
TitleStructural insight into the ESCRT-I-II link and its role in MVB trafficking
ComponentsVPS28-PROV PROTEIN
KeywordsPROTEIN TRANSPORT / NZF FINGER / HIV BUDDING
Function / homology
Function and homology information


ESCRT I complex / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein-containing complex binding
Similarity search - Function
Vps28 C-terminal domain / Vacuolar protein sorting-associated Vps28 / Vacuolar protein sorting-associated, VPS28, N-terminal / Vacuolar protein sorting-associated, VPS28, C-terminal / VPS28, C-terminal domain superfamily / VPS28, N-terminal domain superfamily / VPS28 protein / VPS28 C-terminal domain profile. / VPS28 N-terminal domain profile. / ESCRT assembly domain ...Vps28 C-terminal domain / Vacuolar protein sorting-associated Vps28 / Vacuolar protein sorting-associated, VPS28, N-terminal / Vacuolar protein sorting-associated, VPS28, C-terminal / VPS28, C-terminal domain superfamily / VPS28, N-terminal domain superfamily / VPS28 protein / VPS28 C-terminal domain profile. / VPS28 N-terminal domain profile. / ESCRT assembly domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 28 homolog
Similarity search - Component
Biological speciesXENOPUS LAEVIS (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsGill, D.J. / Teo, H.L. / Sun, J. / Perisic, O. / Veprintsev, D.B. / Emr, S.D. / Williams, R.L.
CitationJournal: Embo J. / Year: 2007
Title: Structural Insight Into the Escrt-I/-II Link and its Role in Mvb Trafficking.
Authors: Gill, D.J. / Teo, H. / Sun, J. / Perisic, O. / Veprintsev, D.B. / Emr, S.D. / Williams, R.L.
History
DepositionNov 16, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
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: VPS28-PROV PROTEIN
B: VPS28-PROV PROTEIN


Theoretical massNumber of molelcules
Total (without water)24,0012
Polymers24,0012
Non-polymers00
Water2,414134
1
A: VPS28-PROV PROTEIN


Theoretical massNumber of molelcules
Total (without water)12,0011
Polymers12,0011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: VPS28-PROV PROTEIN


Theoretical massNumber of molelcules
Total (without water)12,0011
Polymers12,0011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)25.997, 89.713, 40.384
Angle α, β, γ (deg.)90.00, 95.13, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999673, 0.025394, -0.002661), (-0.022532, -0.828357, 0.559745), (0.012009, 0.559623, 0.82866)
Vector: 19.7614, 6.4353, -2.0893)

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Components

#1: Protein VPS28-PROV PROTEIN / VPS28


Mass: 12000.693 Da / Num. of mol.: 2 / Fragment: RESIDUES 123-221
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) XENOPUS LAEVIS (African clawed frog) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q7T0W4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 1.84 Å3/Da / Density % sol: 33.2 %
Crystal growpH: 6.5
Details: 15-25% PEG 600, 0.15M POTASSIUM THIOCYANATE, 0.2M SODIUM CHLORIDE, 0.1M GUANIDINE HYDROCHLORIDE, 0.1M SODIUM CACODYLATE PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 12, 2006 / Details: TORODIAL MIRROR
RadiationMonochromator: KHOZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→44.86 Å / Num. obs: 8573 / % possible obs: 88.3 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.57
Reflection shellResolution: 2.2→2.23 Å / Redundancy: 1.17 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.28 / % possible all: 45.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SE DATASET FROM SEMET SUBSTITUTED CRYSTAL

Resolution: 1.3→44.86 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 0.987 / SU ML: 0.043 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2027 5.1 %RANDOM
Rwork0.2 ---
obs0.202 37809 88.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å2-0.14 Å2
2---0.35 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.3→44.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1638 0 0 134 1772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211679
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.9642261
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4215204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.5224.22290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91915327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.991516
X-RAY DIFFRACTIONr_chiral_restr0.1020.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021266
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.2823
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21176
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.299
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.265
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2680.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1621.51036
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.77321633
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0043707
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3824.5625
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: 1.3→1.33 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.288 90
Rwork0.288 1273
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)
12.5147-6.40660.591516.6869-0.81881.43650.04480.0602-0.1291-0.1173-0.0486-0.33750.07460.13730.00370.1095-0.0069-0.00120.1222-0.01110.101817.64868.63428.5673
20.96920.2173-0.10353.05522.82735.7403-0.01520.0074-0.01560.04270.0619-0.08910.13650.1335-0.04670.04280.0026-0.00330.0410.01010.057612.977920.408440.9041
35.88693.8606-1.55635.86-1.16611.67680.011-0.19820.01420.2317-0.02040.21840.1111-0.17080.00950.07970.0144-0.0060.0792-0.00480.069515.039429.641354.3778
42.63591.39881.90542.48593.04435.3761-0.01040.03120.0009-0.01360.0312-0.0589-0.0030.1041-0.02090.04280.01020.00690.04110.00340.068518.95828.128140.0465
51.5362-0.5973-1.36733.82580.74921.68410.00830.12340.1365-0.1806-0.03940.1371-0.1551-0.13570.03110.1144-0.01020.00360.116-0.00480.09210.96825.458726.9714
64.9963.64914.31796.351-0.06336.54-0.00550.06580.1744-0.0781-0.05720.3626-0.1738-0.34330.06270.06740.0018-0.00040.06080.01160.07457.244231.762134.2682
71.81550.47511.67710.15850.55081.9158-0.06420.03420.18790.0140.0121-0.1012-0.16260.19960.0520.06260.00070.00340.0545-0.0020.068117.611438.176143.8888
83.89491.70241.4363.20781.3483.1288-0.0145-0.15140.09410.0813-0.00490.0333-0.0894-0.05590.01950.0480.0090.00710.041100.04838.733335.486150.756
93.83710.46760.61695.65642.55047.40020.01180.1415-0.1867-0.131-0.10070.28060.2369-0.33760.08890.03230.00970.00590.0450.01220.06892.900923.384636.582
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 11
2X-RAY DIFFRACTION2A12 - 30
3X-RAY DIFFRACTION3A31 - 37
4X-RAY DIFFRACTION4A38 - 52
5X-RAY DIFFRACTION5A53 - 60
6X-RAY DIFFRACTION6A61 - 66
7X-RAY DIFFRACTION7A67 - 81
8X-RAY DIFFRACTION8A82 - 94
9X-RAY DIFFRACTION9A95 - 108

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