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- PDB-3inb: Structure of the measles virus hemagglutinin bound to the CD46 re... -

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Basic information

Entry
Database: PDB / ID: 3inb
TitleStructure of the measles virus hemagglutinin bound to the CD46 receptor
Components
  • Hemagglutinin glycoprotein
  • Membrane cofactor protein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / MEASLES / BETA PROPELLER / ENVELOPE PROTEIN / HEMAGGLUTININ / VIRAL PROTEIN. MEMBRANE COFACTOR PROTEIN / MCP / CD46 / VIRUS RECEPTOR COMPLEX / SCR / COMPLEMENT CONTROL PROTEIN / IMMUNE SYSTEM COMPLEX / Membrane / Transmembrane / Virion / Cell membrane / Glycoprotein / Host-virus interaction / Signal-anchor / Complement pathway / Disease mutation / Disulfide bond / Fertilization / Immune response / Innate immunity / Phosphoprotein / Sushi / VIRAL PROTEIN / IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


sequestering of extracellular ligand from receptor / inner acrosomal membrane / regulation of Notch signaling pathway / negative regulation of complement activation, classical pathway / positive regulation of transforming growth factor beta production / T cell mediated immunity / positive regulation of memory T cell differentiation / positive regulation of regulatory T cell differentiation / positive regulation of interleukin-10 production / single fertilization ...sequestering of extracellular ligand from receptor / inner acrosomal membrane / regulation of Notch signaling pathway / negative regulation of complement activation, classical pathway / positive regulation of transforming growth factor beta production / T cell mediated immunity / positive regulation of memory T cell differentiation / positive regulation of regulatory T cell differentiation / positive regulation of interleukin-10 production / single fertilization / positive regulation of T cell proliferation / complement activation, classical pathway / Regulation of Complement cascade / virus receptor activity / signaling receptor activity / adaptive immune response / host cell surface receptor binding / cadherin binding / symbiont entry into host cell / negative regulation of gene expression / innate immune response / focal adhesion / viral envelope / positive regulation of gene expression / virion attachment to host cell / host cell plasma membrane / virion membrane / cell surface / extracellular space / extracellular exosome / membrane / plasma membrane
Similarity search - Function
: / Membrane cofactor protein CD46 / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Complement Module, domain 1 / Complement Module; domain 1 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. ...: / Membrane cofactor protein CD46 / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Complement Module, domain 1 / Complement Module; domain 1 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Ribbon / Mainly Beta
Similarity search - Domain/homology
Hemagglutinin glycoprotein / Membrane cofactor protein
Similarity search - Component
Biological speciesMeasles virus strain Edmonston
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSantiago, C. / Celma, M.L. / Stehle, T. / Casasnovas, J.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structure of the measles virus hemagglutinin bound to the CD46 receptor
Authors: Santiago, C. / Celma, M.L. / Stehle, T. / Casasnovas, J.M.
History
DepositionAug 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 13, 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
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin glycoprotein
B: Hemagglutinin glycoprotein
C: Membrane cofactor protein
D: Membrane cofactor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,77013
Polymers132,1554
Non-polymers1,6159
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8740 Å2
ΔGint-63 kcal/mol
Surface area49820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.365, 105.833, 208.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain D and (resseq 65:126 )
211chain C and (resseq 65:126 )
112chain A and (resseq 201:238 or resseq 250:262 or resseq...
212chain B and (resseq 201:238 or resseq 250:262 or resseq...

NCS ensembles :
ID
1
2

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Components

#1: Protein Hemagglutinin glycoprotein


Mass: 51559.758 Da / Num. of mol.: 2 / Fragment: Head domain, residues 179-617
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Measles virus strain Edmonston / Strain: Edmonston / Gene: H / Plasmid: PBJ5-GS / Cell line (production host): Ovary Cells / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): Cho-Lec 3281 / References: UniProt: P08362
#2: Protein Membrane cofactor protein / Trophoblast leukocyte common antigen / TLX


Mass: 14517.551 Da / Num. of mol.: 2 / Fragment: Sushi domains 1 and 2, residues 35-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD46, MCP, MIC10 / Plasmid: PBJ5-GS / Cell line (production host): Ovary Cells / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): Cho-Lec 3281 / References: UniProt: P15529
#3: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
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
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.4 Å3/Da / Density % sol: 63.82 %
Crystal growTemperature: 293 K / pH: 6.5
Details: 12% PEG-8000, 0.2 M Ammonium Sulphate 2% PEG-400, 1% 1,2,3 heptanetriol, 1 mM Sodium Tungstate, 0.1 M Mes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.845
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 31, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.845 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. obs: 33285 / % possible obs: 96 % / Redundancy: 3.7 % / Biso Wilson estimate: 101.02 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 22.7
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.1 / % possible all: 96

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2ZB6, 1CKL, and 2O39

2zb6

1ckl

2o39


Resolution: 3.1→14.976 Å / SU ML: 0.43 / σ(F): 1.38 / Phase error: 32.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2592 1588 4.98 %
Rwork0.2266 --
obs0.2283 31869 96.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.677 Å2 / ksol: 0.256 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-56.3438 Å2-0 Å2-0 Å2
2---40.0922 Å20 Å2
3----16.2516 Å2
Refinement stepCycle: LAST / Resolution: 3.1→14.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8235 0 99 8 8342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088588
X-RAY DIFFRACTIONf_angle_d1.49711673
X-RAY DIFFRACTIONf_dihedral_angle_d26.6245144
X-RAY DIFFRACTIONf_chiral_restr0.1121287
X-RAY DIFFRACTIONf_plane_restr0.0081473
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11D491X-RAY DIFFRACTIONPOSITIONAL
12C491X-RAY DIFFRACTIONPOSITIONAL0.08
21A2600X-RAY DIFFRACTIONPOSITIONAL
22B2600X-RAY DIFFRACTIONPOSITIONAL0.046
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.19910.44651480.40832706X-RAY DIFFRACTION96
3.1991-3.31230.40411260.36942710X-RAY DIFFRACTION96
3.3123-3.44340.32921400.32842706X-RAY DIFFRACTION96
3.4434-3.5980.35041480.2882732X-RAY DIFFRACTION96
3.598-3.78480.29371370.27462731X-RAY DIFFRACTION96
3.7848-4.01770.25621660.23662707X-RAY DIFFRACTION96
4.0177-4.32090.23951340.20442762X-RAY DIFFRACTION96
4.3209-4.74320.24351460.17472772X-RAY DIFFRACTION96
4.7432-5.40110.20281370.1722774X-RAY DIFFRACTION96
5.4011-6.70180.24151590.19922807X-RAY DIFFRACTION96
6.7018-14.97620.21951470.19642874X-RAY DIFFRACTION95
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined4.3477-3.0623-1.9549.07931.09482.90490.74080.75490.0134-2.7767-0.60391.0231-0.1844-0.48680.0180.60630.3106-0.24060.68380.06240.392-17.944759.873129.0226
23.0519-1.38160.49696.12960.2873.69120.24210.211-0.2531-1.5989-0.0636-1.0418-0.04670.56120.00010.70250.02240.40820.631-0.09180.7379
30.99640.9046-0.19351.2183-0.09050.670.08490.5522-0.2418-1.06760.1009-0.1560.65310.43150.00061.72260.29250.20550.9185-0.11251.1147
40.7786-0.05420.00871.17960.26790.90180.45230.51760.4939-1.0637-0.22390.0251-0.3858-0.11260.00021.84360.29470.2121.02890.25550.9058
Refinement TLS groupSelection details: chain D

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