PDB-3d11: Crystal Structures of the Nipah G Attachment Glycoprotein

ID or keywords:

Entry

Database: PDB / ID: 3d11

Title

Crystal Structures of the Nipah G Attachment Glycoprotein

Components

Hemagglutinin-neuraminidase

Keywords

HYDROLASE / beta propeller / Envelope protein / Glycoprotein / Hemagglutinin / Membrane / Signal-anchor / Transmembrane / Virion

Function / homology

Function and homology information

membrane fusion involved in viral entry into host cell / exo-alpha-sialidase activity / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / identical protein binding / membrane
Similarity search - Function

Biological species

Nipah virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.306 Å

Authors

Xu, K. / Rajashankar, K.R. / Chan, Y.P. / Himanen, P. / Broder, C.C. / Nikolov, D.B.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Host cell recognition by the henipaviruses: crystal structures of the Nipah G attachment glycoprotein and its complex with ephrin-B3.
Authors: Xu, K. / Rajashankar, K.R. / Chan, Y.P. / Himanen, J.P. / Broder, C.C. / Nikolov, D.B.

History

Deposition	May 2, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 19, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Non-polymer description / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software
Revision 2.0	Jul 29, 2020	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_struct_special_symmetry / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 / _struct_ref_seq_dif.details Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1	Nov 13, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3d11.cif.gz	109.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3d11.ent.gz	82.5 KB	Display	PDB format
PDBx/mmJSON format	3d11.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3d11_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	3d11_full_validation.pdf.gz	1.5 MB	Display
Data in XML	3d11_validation.xml.gz	25.5 KB	Display
Data in CIF	3d11_validation.cif.gz	34.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d1/3d11 ftp://data.pdbj.org/pub/pdb/validation_reports/d1/3d11	HTTPS FTP

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Related structure data

Related structure data	3d12C C: citing same article (ref.)
Similar structure data	6dim-2 1e72-d 4k1c-1 5o5k-1 4kdp-2 6lsc-d 1e6s-d 1e70-d 3uab-d 5nop-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#231 - Mar 2019 Measles Virus Proteins similarity (3) #76 - Apr 2006 Hemagglutinin similarity (1) #113 - May 2009 Influenza Neuraminidase similarity (1)

Deposited unit

A: Hemagglutinin-neuraminidase

hetero molecules

52.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	130.161, 130.161, 130.161
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	198
Space group name H-M	P2₁3

Components on special symmetry positions

ID	Model	Components
1	1	A-4- IOD
2	1	A-1460- HOH

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Protein , 1 types, 1 molecules A

#1: Protein	Hemagglutinin-neuraminidase Mass: 47966.520 Da / Num. of mol.: 1 / Fragment: UNP residues 176-602 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nipah virus / Gene: HN / Plasmid: pAcGP67 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi5 / References: UniProt: Q9IH62, exo-alpha-sialidase

#1: Protein

Hemagglutinin-neuraminidase

Mass: 47966.520 Da / Num. of mol.: 1 / Fragment: UNP residues 176-602
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Nipah virus / Gene: HN / Plasmid: pAcGP67 / Production host:

Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi5 / References: UniProt: Q9IH62, exo-alpha-sialidase

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Sugars , 3 types, 4 molecules

#2: 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.: 2
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGlcpNAcb1-4DGlcpNAcb1-	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1	WURCS	PDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}	LINUCS	PDB-CARE

#3: Polysaccharide

beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...

Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DManpb1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-2-3/a4-b1_b4-c1_c3-d1_c6-e1	WURCS	PDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}	LINUCS	PDB-CARE

#4: 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

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

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Non-polymers , 2 types, 229 molecules

#5: Chemical	ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: I
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.84 Å³/Da / Density % sol: 67.98 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: PEG 3350, KI, pH 6.8, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-C / Wavelength: 1.5498 Å

Detector

Date: Aug 18, 2007

Radiation

Monochromator: S / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5498 Å / Relative weight: 1

Reflection

Resolution: 2.3→40 Å / Num. obs: 55607 / % possible obs: 88.5 % / Redundancy: 3.3 % / R_merge(I) obs: 0.086 / Net I/σ(I): 12.7

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
2.3-2.38	1.4	0.357	1	42.6
2.38-2.48	1.9	0.318	1	66.8
2.48-2.59	2.6	0.293	1	82.9
2.59-2.73	3.4	0.257	1	94.6
2.73-2.9	3.7	0.185	1	99.2
2.9-3.12	3.7	0.127	1	99.6
3.12-3.44	3.7	0.096	1	99.9
3.44-3.93	3.7	0.083	1	100
3.93-4.95	3.6	0.077	1	100
4.95-40	3.7	0.06	1	99.5

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHENIX		refinement
PDB_EXTRACT	3.005	data extraction
HKL-2000		data reduction
HKL-2000		data scaling
SHELXS		phasing

Refinement

Resolution: 2.306→39.245 Å / Stereochemistry target values: ml

	R_factor	Num. reflection	% reflection
R_free	0.257	2519	4.76 %
R_work	0.228	-	-
obs	-	52865	84.2 %

Solvent computation

B_sol: 38.278 Å² / k_sol: 0.346 e/Å³

Displacement parameters

B_iso mean: 42.51 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0 Å²	-0 Å²	-0 Å²
2-	-	0 Å²	0 Å²
3-	-	-	0 Å²

Refinement step

Cycle: LAST / Resolution: 2.306→39.245 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3361	0	150	210	3721

Refine LS restraints

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	f_bond_d	0.005
X-RAY DIFFRACTION	f_angle_d	0.757
X-RAY DIFFRACTION	f_dihedral_angle_d	16.421
X-RAY DIFFRACTION	f_chiral_restr	0.056
X-RAY DIFFRACTION	f_plane_restr	0.003

LS refinement shell

Resolution (Å)	R_factor R_work	Num. reflection R_work	Refine-ID	Total num. of bins used	% reflection obs (%)
2.306-2.314	0.324	132	X-RAY DIFFRACTION	101	21
2.314-2.322	0.336	176	X-RAY DIFFRACTION	101	27
2.322-2.33	0.34	166	X-RAY DIFFRACTION	101	25
2.33-2.338	0.288	194	X-RAY DIFFRACTION	101	35
2.338-2.346	0.273	200	X-RAY DIFFRACTION	101	32
2.346-2.354	0.338	237	X-RAY DIFFRACTION	101	36
2.354-2.362	0.308	238	X-RAY DIFFRACTION	101	39
2.362-2.371	0.309	241	X-RAY DIFFRACTION	101	42
2.371-2.379	0.296	309	X-RAY DIFFRACTION	101	45
2.379-2.388	0.306	284	X-RAY DIFFRACTION	101	51
2.388-2.397	0.289	329	X-RAY DIFFRACTION	101	50
2.397-2.406	0.307	294	X-RAY DIFFRACTION	101	49
2.406-2.415	0.262	344	X-RAY DIFFRACTION	101	52
2.415-2.424	0.317	338	X-RAY DIFFRACTION	101	55
2.424-2.433	0.313	315	X-RAY DIFFRACTION	101	55
2.433-2.443	0.307	350	X-RAY DIFFRACTION	101	55
2.443-2.453	0.273	432	X-RAY DIFFRACTION	101	62
2.453-2.462	0.301	322	X-RAY DIFFRACTION	101	59
2.462-2.472	0.271	383	X-RAY DIFFRACTION	101	61
2.472-2.482	0.298	412	X-RAY DIFFRACTION	101	65
2.482-2.493	0.275	393	X-RAY DIFFRACTION	101	64
2.493-2.503	0.268	434	X-RAY DIFFRACTION	101	66
2.503-2.514	0.289	387	X-RAY DIFFRACTION	101	69
2.514-2.525	0.293	467	X-RAY DIFFRACTION	101	72
2.525-2.536	0.283	427	X-RAY DIFFRACTION	101	71
2.536-2.547	0.276	430	X-RAY DIFFRACTION	101	69
2.547-2.558	0.276	462	X-RAY DIFFRACTION	101	71
2.558-2.57	0.271	419	X-RAY DIFFRACTION	101	73
2.57-2.582	0.273	472	X-RAY DIFFRACTION	101	75
2.582-2.594	0.312	511	X-RAY DIFFRACTION	101	78
2.594-2.606	0.274	476	X-RAY DIFFRACTION	101	77
2.606-2.619	0.288	473	X-RAY DIFFRACTION	101	77
2.619-2.631	0.278	468	X-RAY DIFFRACTION	101	75
2.631-2.644	0.281	486	X-RAY DIFFRACTION	101	80
2.644-2.658	0.286	510	X-RAY DIFFRACTION	101	80
2.658-2.671	0.272	521	X-RAY DIFFRACTION	101	85
2.671-2.685	0.281	506	X-RAY DIFFRACTION	101	83
2.685-2.699	0.265	547	X-RAY DIFFRACTION	101	87
2.699-2.714	0.274	568	X-RAY DIFFRACTION	101	87
2.714-2.728	0.248	511	X-RAY DIFFRACTION	101	87
2.728-2.743	0.286	504	X-RAY DIFFRACTION	101	81
2.743-2.759	0.292	534	X-RAY DIFFRACTION	101	85
2.759-2.775	0.244	587	X-RAY DIFFRACTION	101	90
2.775-2.791	0.267	514	X-RAY DIFFRACTION	101	87
2.791-2.807	0.267	540	X-RAY DIFFRACTION	101	87
2.807-2.824	0.264	568	X-RAY DIFFRACTION	101	88
2.824-2.842	0.271	532	X-RAY DIFFRACTION	101	89
2.842-2.859	0.257	541	X-RAY DIFFRACTION	101	90
2.859-2.877	0.232	573	X-RAY DIFFRACTION	101	92
2.877-2.896	0.27	591	X-RAY DIFFRACTION	101	88
2.896-2.915	0.273	564	X-RAY DIFFRACTION	101	93
2.915-2.935	0.253	540	X-RAY DIFFRACTION	101	92
2.935-2.955	0.229	563	X-RAY DIFFRACTION	101	88
2.955-2.976	0.234	558	X-RAY DIFFRACTION	101	88
2.976-2.997	0.256	567	X-RAY DIFFRACTION	101	92
2.997-3.019	0.235	565	X-RAY DIFFRACTION	101	93
3.019-3.042	0.261	552	X-RAY DIFFRACTION	101	93
3.042-3.066	0.266	600	X-RAY DIFFRACTION	101	92
3.066-3.09	0.227	565	X-RAY DIFFRACTION	101	94
3.09-3.115	0.243	551	X-RAY DIFFRACTION	101	92
3.115-3.14	0.244	569	X-RAY DIFFRACTION	101	93
3.14-3.167	0.244	602	X-RAY DIFFRACTION	101	91
3.167-3.194	0.23	587	X-RAY DIFFRACTION	101	93
3.194-3.223	0.245	571	X-RAY DIFFRACTION	101	94
3.223-3.253	0.221	591	X-RAY DIFFRACTION	101	95
3.253-3.283	0.201	579	X-RAY DIFFRACTION	101	93
3.283-3.315	0.227	564	X-RAY DIFFRACTION	101	92
3.315-3.348	0.212	630	X-RAY DIFFRACTION	101	97
3.348-3.383	0.216	575	X-RAY DIFFRACTION	101	94
3.383-3.419	0.218	585	X-RAY DIFFRACTION	101	96
3.419-3.456	0.199	597	X-RAY DIFFRACTION	101	96
3.456-3.495	0.193	564	X-RAY DIFFRACTION	101	96
3.495-3.536	0.194	617	X-RAY DIFFRACTION	101	94
3.536-3.58	0.189	581	X-RAY DIFFRACTION	101	95
3.58-3.625	0.207	591	X-RAY DIFFRACTION	101	95
3.625-3.672	0.191	591	X-RAY DIFFRACTION	101	96
3.672-3.723	0.193	597	X-RAY DIFFRACTION	101	95
3.723-3.776	0.186	590	X-RAY DIFFRACTION	101	95
3.776-3.832	0.19	624	X-RAY DIFFRACTION	101	93
3.832-3.892	0.193	522	X-RAY DIFFRACTION	101	93
3.892-3.956	0.196	594	X-RAY DIFFRACTION	101	94
3.956-4.024	0.196	575	X-RAY DIFFRACTION	101	95
4.024-4.097	0.169	613	X-RAY DIFFRACTION	101	92
4.097-4.176	0.165	556	X-RAY DIFFRACTION	101	93
4.176-4.261	0.177	591	X-RAY DIFFRACTION	101	96
4.261-4.353	0.162	594	X-RAY DIFFRACTION	101	93
4.353-4.455	0.153	571	X-RAY DIFFRACTION	101	92
4.455-4.566	0.161	571	X-RAY DIFFRACTION	101	95
4.566-4.689	0.171	587	X-RAY DIFFRACTION	101	92
4.689-4.827	0.171	604	X-RAY DIFFRACTION	101	96
4.827-4.982	0.191	577	X-RAY DIFFRACTION	101	94
4.982-5.16	0.189	580	X-RAY DIFFRACTION	101	94
5.16-5.366	0.21	594	X-RAY DIFFRACTION	101	95
5.366-5.61	0.19	599	X-RAY DIFFRACTION	101	95
5.61-5.905	0.226	621	X-RAY DIFFRACTION	101	98
5.905-6.273	0.229	577	X-RAY DIFFRACTION	101	96
6.273-6.755	0.259	594	X-RAY DIFFRACTION	101	96
6.755-7.431	0.275	594	X-RAY DIFFRACTION	101	95
7.431-8.497	0.27	593	X-RAY DIFFRACTION	101	95
8.497-10.669	0.252	601	X-RAY DIFFRACTION	101	94
10.669-39.251	0.338	560	X-RAY DIFFRACTION	101	90

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