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

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Basic information

Entry
Database: PDB / ID: 3alz
TitleCrystal structure of the measles virus hemagglutinin bound to its cellular receptor SLAM (Form I)
Components
  • CDw150
  • Hemagglutinin
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 / signaling receptor activity / host cell surface receptor binding / receptor ligand activity / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / cell surface ...lymphocyte activation / signaling receptor activity / host cell surface receptor binding / receptor ligand activity / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / cell surface / membrane / plasma membrane
Similarity search - Function
Signaling lymphocytic activation molecule, N-terminal / Signaling lymphocytic activation molecule (SLAM) protein / : / : / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like fold
Similarity search - Domain/homology
Hemagglutinin glycoprotein / Hemagglutinin glycoprotein / Signaling lymphocytic activation molecule
Similarity search - Component
Biological speciesMeasles virus
Saguinus oedipus (cotton-top tamarin)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.515 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 11, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 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_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: CDw150
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1124
Polymers70,6702
Non-polymers4422
Water00
1
A: Hemagglutinin
B: CDw150
hetero molecules

A: Hemagglutinin
B: CDw150
hetero molecules

A: Hemagglutinin
B: CDw150
hetero molecules

A: Hemagglutinin
B: CDw150
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,44816
Polymers282,6788
Non-polymers1,7708
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x+y-1,-x,z1
crystal symmetry operation11_454-x+y-1,y,-z-1/21
crystal symmetry operation12_564x,x-y+1,-z-1/21
2
A: Hemagglutinin
B: CDw150
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)426,67224
Polymers424,01812
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_554-y,-x,-z-1/21
crystal symmetry operation11_454-x+y-1,y,-z-1/21
crystal symmetry operation12_564x,x-y+1,-z-1/21
Buried area26750 Å2
ΔGint-111 kcal/mol
Surface area133100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.119, 208.119, 182.127
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


Mass: 53423.656 Da / Num. of mol.: 1 / Fragment: head domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Measles virus / Strain: Edmonston B / Gene: Hemagglutinin / Plasmid: pCA7 / Cell line (production host): HEK293SGnTI(-) / Production host: Homo sapiens (human) / References: UniProt: E2RZS2, UniProt: P08362*PLUS
#2: Protein CDw150 / CD150 / Signaling lymphocytic activation molecule 1


Mass: 17245.938 Da / Num. of mol.: 1 / Fragment: V domain, residues 1-140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saguinus oedipus (cotton-top tamarin) / Strain: B95a / Gene: SLAM (CD150) / Plasmid: pCA7 / Cell line (production host): HEK293SGnTI(-) / Production host: Homo sapiens (human) / References: UniProt: Q9GJT3
#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.: 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
Has protein modificationY

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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: 8.055825 Å3/Da / Density % sol: 84.731544 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES pH6.5, 0.75M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.5→30.04 Å / Num. obs: 14397 / % possible obs: 100 % / Redundancy: 15.5 % / Biso Wilson estimate: 154.7 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 15.4
Reflection shellResolution: 4.5→4.66 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 4.9 / Num. unique all: 1396 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZB6

2zb6


Resolution: 4.515→30.039 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7401 / SU ML: 0.72 / σ(F): 1.34 / Phase error: 31.44 / Stereochemistry target values: ML
Details: DUE TO LOW RESOLUTION, THE REFINEMENT PROTOCOL WAS LIMITED TO THE FOLLOWING THREE STEPS AFTER MOLECULAR REPLACEMENT. 1. RIGID BODY REFINEMENT OF INDIVIDUAL DOMAINS 2. TLS REFINEMENT OF ...Details: DUE TO LOW RESOLUTION, THE REFINEMENT PROTOCOL WAS LIMITED TO THE FOLLOWING THREE STEPS AFTER MOLECULAR REPLACEMENT. 1. RIGID BODY REFINEMENT OF INDIVIDUAL DOMAINS 2. TLS REFINEMENT OF SELECTED PORTIONS 3. STRUCTURE REGULARIZATION TO AVOID MINOR CLASHES. WE PERFORMED NO INDIVIDUAL ATOM REFINEMENT.
RfactorNum. reflection% reflection
Rfree0.3376 710 5.03 %
Rwork0.3258 13405 -
obs0.3263 14115 99.84 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 199.342 Å2 / ksol: 0.301 e/Å3
Displacement parametersBiso max: 712.58 Å2 / Biso mean: 271.8932 Å2 / Biso min: 128.63 Å2
Baniso -1Baniso -2Baniso -3
1-1.5731 Å20 Å2-0 Å2
2--1.5731 Å2-0 Å2
3----3.1463 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.76 Å0.6 Å
Luzzati d res low-5 Å
Luzzati sigma a1.85 Å1.38 Å
Refinement stepCycle: LAST / Resolution: 4.515→30.039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4135 0 28 0 4163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094271
X-RAY DIFFRACTIONf_angle_d1.5665794
X-RAY DIFFRACTIONf_dihedral_angle_d16.2261578
X-RAY DIFFRACTIONf_chiral_restr0.104654
X-RAY DIFFRACTIONf_plane_restr0.009730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.5151-4.86240.36221650.34882585X-RAY DIFFRACTION99
4.8624-5.34920.30751310.31872624X-RAY DIFFRACTION100
5.3492-6.11760.35791410.30022657X-RAY DIFFRACTION100
6.1176-7.68610.35631550.35382672X-RAY DIFFRACTION100
7.6861-30.040.32081180.31882867X-RAY DIFFRACTION100
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)
12.62881.93690.63350.9423-0.3574.6579-0.2926-0.2635-0.94470.0441-0.2081-0.50091.13610.0790.42871.78120.09520.10171.00160.19311.4349-88.737134.5001-26.2282
20.2274-0.82130.18431.48480.18980.21620.66940.05940.55780.27660.6039-0.94820.49260.9686-0.71924.1535-0.3229-0.28411.60210.52382.0563-98.59879.5704-5.0062
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA188 - 901
2X-RAY DIFFRACTION2chain BB32 - 140

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