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- PDB-3alw: Crystal structure of the measles virus hemagglutinin bound to its... -

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Basic information

Entry
Database: PDB / ID: 3alw
TitleCrystal structure of the measles virus hemagglutinin bound to its cellular receptor SLAM (Form I, MV-H-SLAM(N102H/R108Y) fusion)
ComponentsHemagglutinin, CDw150
Keywordsviral protein/membrane protein / viral protein-receptor complex / six-bladed beta-propeller fold / Immunoglobulin fold / beta-sandwich / viral protein-membrane protein complex
Function / homology
Function and homology information


lymphocyte activation / host cell membrane / positive regulation of type II interferon production / signaling receptor activity / host cell surface receptor binding / symbiont entry into host cell / external side of plasma membrane / viral envelope / virion attachment to host cell / host cell plasma membrane ...lymphocyte activation / host cell membrane / positive regulation of type II interferon production / signaling receptor activity / host cell surface receptor binding / symbiont entry into host cell / external side of plasma membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
: / Signaling lymphocytic activation molecule, N-terminal / Signaling lymphocytic activation molecule (SLAM) protein / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Ig-like domain profile. ...: / Signaling lymphocytic activation molecule, N-terminal / Signaling lymphocytic activation molecule (SLAM) protein / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Hemagglutinin glycoprotein / Hemagglutinin glycoprotein / CDw150
Similarity search - Component
Biological speciesMeasles virus
synthetic construct (others)
Saguinus oedipus (cotton-top tamarin)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.55 Å
AuthorsHashiguchi, T. / Ose, T. / Kubota, M. / Maita, N. / Kamishikiryo, J. / Maenaka, K. / Yanagi, Y.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Structure of the measles virus hemagglutinin bound to its cellular receptor SLAM
Authors: Hashiguchi, T. / Ose, T. / Kubota, M. / Maita, N. / Kamishikiryo, J. / Maenaka, K. / Yanagi, Y.
History
DepositionAug 9, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 28, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq / struct_ref_seq_dif / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Hemagglutinin, CDw150
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5213
Polymers62,0791
Non-polymers4422
Water00
1
A: Hemagglutinin, CDw150
hetero molecules

A: Hemagglutinin, CDw150
hetero molecules

A: Hemagglutinin, CDw150
hetero molecules

A: Hemagglutinin, CDw150
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,08512
Polymers248,3154
Non-polymers1,7708
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation11_455-x+y-1,y,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
2
A: Hemagglutinin, CDw150
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)375,12718
Polymers372,4736
Non-polymers2,65412
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
crystal symmetry operation10_555-y,-x,-z+1/21
crystal symmetry operation11_455-x+y-1,y,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
Buried area10210 Å2
ΔGint-71 kcal/mol
Surface area123990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.912, 209.912, 180.538
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Hemagglutinin, CDw150 / CD150 / Signaling lymphocytic activation molecule 1


Mass: 62078.816 Da / Num. of mol.: 1
Fragment: Hemagglutinin head domain/CD150 V domain, UNP reisudes 30-140
Mutation: N692H, R698Y (CDw150)
Source method: isolated from a genetically manipulated source
Details: MV-H/SLAM fusion protein
Source: (gene. exp.) Measles virus, (gene. exp.) synthetic construct (others), (gene. exp.) Saguinus oedipus (cotton-top tamarin)
Strain: Edmonston B, B95a / Gene: Hemagglutinin, CD150 / Plasmid: pCA7 / Cell line (production host): HEK293SGnTI(-) / Production host: Homo sapiens (human)
References: UniProt: E2RZS2, UniProt: Q9GJT3, 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


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
Sequence detailsTHE GGGSGGGSGGGS(RESIDUES 608-619) AT THE MIDDLE OF THE SEQUENCE IS LINKER REGION.

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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: 9.990449 Å3/Da / Density % sol: 87.68824 %
Crystal growTemperature: 293 K / Method: vapor diffusion, floating drop / pH: 5.8
Details: 0.1M imidazole pH5.8, 0.5M (NH4)2SO4, 0.7M Li2SO4, 3% ethylene glycol, VAPOR DIFFUSION, FLOATING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.55→30 Å / Num. obs: 28716 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20 % / Biso Wilson estimate: 78.3 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 38.6
Reflection shellResolution: 3.55→3.68 Å / Redundancy: 20 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 6.5 / Num. unique all: 2831 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZB6

2zb6


Resolution: 3.55→29.89 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 4911388.71 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1447 5.1 %RANDOM
Rwork0.25 ---
obs0.25 28487 98.8 %-
all-28894 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 99.3884 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 138.9 Å2
Baniso -1Baniso -2Baniso -3
1-13.37 Å2-0 Å20 Å2
2--13.37 Å20 Å2
3----26.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.6 Å0.5 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 3.55→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4005 0 28 0 4033
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.55→3.68 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.356 147 5.2 %
Rwork0.342 2661 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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