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- PDB-6cmi: Crystal Structure of the Hendra Virus Attachment G Glycoprotein B... -

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Basic information

Entry
Database: PDB / ID: 6cmi
TitleCrystal Structure of the Hendra Virus Attachment G Glycoprotein Bound to a Potent Cross-Reactive Neutralizing Human Monoclonal Antibody m102.3
Components
  • Glycoprotein G
  • IgG Heavy chain
  • m102.3 light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Hendra virus / attachment / glycoprotein / cross-reactive / neutralizing / antibody / ANTIVIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


exo-alpha-sialidase activity / host cell surface / 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-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHendra virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.72 Å
AuthorsXu, K. / Nikolov, D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI054715 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI077995 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS38586 United States
CitationJournal: PLoS Pathog. / Year: 2013
Title: Crystal structure of the Hendra virus attachment G glycoprotein bound to a potent cross-reactive neutralizing human monoclonal antibody.
Authors: Xu, K. / Rockx, B. / Xie, Y. / DeBuysscher, B.L. / Fusco, D.L. / Zhu, Z. / Chan, Y.P. / Xu, Y. / Luu, T. / Cer, R.Z. / Feldmann, H. / Mokashi, V. / Dimitrov, D.S. / Bishop-Lilly, K.A. / ...Authors: Xu, K. / Rockx, B. / Xie, Y. / DeBuysscher, B.L. / Fusco, D.L. / Zhu, Z. / Chan, Y.P. / Xu, Y. / Luu, T. / Cer, R.Z. / Feldmann, H. / Mokashi, V. / Dimitrov, D.S. / Bishop-Lilly, K.A. / Broder, C.C. / Nikolov, D.B.
History
DepositionMar 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Derived calculations / Structure summary
Category: entity / pdbx_struct_assembly_gen ...entity / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct
Item: _entity.pdbx_description / _pdbx_struct_assembly_prop.value / _struct.pdbx_descriptor
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Glycoprotein G
C: m102.3 light chain
D: IgG Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,0968
Polymers96,5613
Non-polymers2,5355
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8010 Å2
ΔGint9 kcal/mol
Surface area38030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.275, 148.533, 185.485
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Antibody , 2 types, 2 molecules CD

#2: Antibody m102.3 light chain


Mass: 23431.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody IgG Heavy chain


Mass: 25141.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Non-polymers , 2 types, 55 molecules B

#1: Protein Glycoprotein G


Mass: 47988.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hendra virus / Production host: Homo sapiens (human) / References: UniProt: O89343
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 3 types, 5 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1040.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-3][LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-1-3-4-2/a3-b1_a4-c1_a6-f1_c4-d1_d3-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: 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.: 1
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

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Details

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: 3.19 Å3/Da / Density % sol: 61.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 15% PEG4000, 0.1M Hepes pH 7.0, 0.1M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.72→50 Å / Num. obs: 33472 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 56.34 Å2 / Rmerge(I) obs: 0.087 / Χ2: 1.058 / Net I/σ(I): 10.8 / Num. measured all: 220117
Reflection shellResolution: 2.72→2.8 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.637 / Num. unique obs: 2946 / Χ2: 0.621 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.72→35.992 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2459 1694 5.06 %
Rwork0.1955 --
obs0.1981 33466 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.72→35.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6733 0 168 54 6955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047085
X-RAY DIFFRACTIONf_angle_d0.839669
X-RAY DIFFRACTIONf_dihedral_angle_d6.2084209
X-RAY DIFFRACTIONf_chiral_restr0.0511112
X-RAY DIFFRACTIONf_plane_restr0.0051220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.72-2.79560.39581090.32132472X-RAY DIFFRACTION93
2.7956-2.88580.35761540.28262617X-RAY DIFFRACTION100
2.8858-2.98890.31171410.25872618X-RAY DIFFRACTION100
2.9889-3.10850.30991340.25312628X-RAY DIFFRACTION100
3.1085-3.24990.33481470.25162642X-RAY DIFFRACTION100
3.2499-3.42120.31461360.23352647X-RAY DIFFRACTION100
3.4212-3.63530.27451320.21362661X-RAY DIFFRACTION100
3.6353-3.91570.26621530.20382625X-RAY DIFFRACTION100
3.9157-4.30920.22091290.17062684X-RAY DIFFRACTION100
4.3092-4.93130.19671540.1462672X-RAY DIFFRACTION100
4.9313-6.20780.1921600.1642685X-RAY DIFFRACTION100
6.2078-35.99480.19841450.17142821X-RAY DIFFRACTION100

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