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- PDB-5wb1: Ligand-free US28 with stabilizing intracellular nanobody -

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Basic information

Entry
Database: PDB / ID: 5wb1
TitleLigand-free US28 with stabilizing intracellular nanobody
ComponentsEnvelope protein US28, nanobody 7 fusion protein
KeywordsMEMBRANE PROTEIN / chemokine receptor
Function / homology
Function and homology information


: / chemokine receptor activity / virus-mediated perturbation of host defense response / chemotaxis / viral envelope / host cell plasma membrane / membrane
Similarity search - Function
Chemokine receptor family / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
G-protein coupled receptor homolog US28 / Envelope protein US28
Similarity search - Component
Biological speciesHuman cytomegalovirus
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.508 Å
AuthorsJude, K.M. / Burg, J.S. / Garcia, K.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097015 United States
CitationJournal: Elife / Year: 2018
Title: Viral GPCR US28 can signal in response to chemokine agonists of nearly unlimited structural degeneracy.
Authors: Miles, T.F. / Spiess, K. / Jude, K.M. / Tsutsumi, N. / Burg, J.S. / Ingram, J.R. / Waghray, D. / Hjorto, G.M. / Larsen, O. / Ploegh, H.L. / Rosenkilde, M.M. / Garcia, K.C.
History
DepositionJun 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Envelope protein US28, nanobody 7 fusion protein


Theoretical massNumber of molelcules
Total (without water)51,8281
Polymers51,8281
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.600, 38.300, 99.800
Angle α, β, γ (deg.)90.00, 107.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Envelope protein US28, nanobody 7 fusion protein / / US28 protein


Mass: 51827.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human cytomegalovirus, (gene. exp.) Lama glama (llama)
Gene: US28 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q80KM9, UniProt: P69333*PLUS

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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: 2.73 Å3/Da / Density % sol: 54.95 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 37-41% PEG300, 100 mM MES, pH 6.2-6.6, 100 mM ammonium tartrate in monoolein:cholesterol (9:1)
PH range: 6.2-6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 20, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.49→50 Å / Num. obs: 7426 / % possible obs: 99.2 % / Redundancy: 6.3 % / Biso Wilson estimate: 84.9 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.0221 / Rpim(I) all: 0.0241 / Net I/σ(I): 6.85
Reflection shellResolution: 3.49→3.58 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.392 / Mean I/σ(I) obs: 0.94 / Num. unique obs: 491 / CC1/2: 0.606 / Rrim(I) all: 1.583 / % possible all: 91.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSMarch 1, 2015data reduction
XSCALEMarch 1, 2015data scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4XT1
Resolution: 3.508→29.844 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.58
RfactorNum. reflection% reflectionSelection details
Rfree0.2889 711 9.97 %Random selection
Rwork0.2423 ---
obs0.2471 7129 97.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.508→29.844 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3291 0 0 0 3291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023379
X-RAY DIFFRACTIONf_angle_d0.54611
X-RAY DIFFRACTIONf_dihedral_angle_d9.811965
X-RAY DIFFRACTIONf_chiral_restr0.038541
X-RAY DIFFRACTIONf_plane_restr0.003564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5083-3.77870.35581300.33271134X-RAY DIFFRACTION88
3.7787-4.1580.38161420.28621304X-RAY DIFFRACTION100
4.158-4.75760.27081420.23961306X-RAY DIFFRACTION100
4.7576-5.98620.3291480.25511305X-RAY DIFFRACTION100
5.9862-29.8450.22651490.19541369X-RAY DIFFRACTION100

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