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- PDB-2rkc: Crystal structure of the measles virus hemagglutinin -

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Basic information

Entry
Database: PDB / ID: 2rkc
TitleCrystal structure of the measles virus hemagglutinin
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / hemagglutinin / measles virus / Envelope protein / Membrane / Transmembrane / Virion
Function / homology
Function and homology information


membrane => GO:0016020 / host cell surface receptor binding / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
: / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Hemagglutinin glycoprotein / Hemagglutinin glycoprotein
Similarity search - Component
Biological speciesMeasles virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.7 Å
AuthorsColf, L.A. / Juo, Z.S. / Garcia, K.C.
CitationJournal: To be Published
Title: Structure of the measles virus hemagglutinin: implications for host cell receptor attachment.
Authors: Colf, L.A. / Juo, Z.S. / Garcia, K.C.
History
DepositionOct 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6753
Polymers51,2321
Non-polymers4422
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.197, 134.197, 100.647
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Hemagglutinin /


Mass: 51232.430 Da / Num. of mol.: 1 / Fragment: Extracellular domain (156-617) / Mutation: N238I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Measles virus / Genus: Morbillivirus / Strain: Edmonston strain / Gene: Hemagglutinin / Plasmid: pVL1393 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi 5 / References: UniProt: Q83531, UniProt: P08362*PLUS
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.42 Å3/Da / Density % sol: 72.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 1.2M sodium dihydrogen phosphate, 0.3M di-potassium hydrogen phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.072, 1.072
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 11, 2007
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. all: 48443 / Num. obs: 25665 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 58.7 Å2 / Rfree details: 0.05 / Rmerge(I) obs: 0.083 / Net I/σ(I): 15
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 2.9 / Num. unique all: 7174 / Rsym value: 0.538 / % possible all: 99.9

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Processing

Software
NameClassification
HKL-2000data collection
SHARPphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.7→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2514 1279 5 %Random
Rwork0.2221 ---
all-25810 --
obs-25665 99.4 %-
Refinement stepCycle: LAST / Resolution: 2.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3109 0 28 66 3203
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.452

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