9lue

Cryo-EM structure of the Nipah G head domain in complex with three Fabs

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glycoprotein G

Henipavirus nipahense

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	NIV LN3D3 Fab Light Chain × 1 NiV S2B10 Fab Heavy Chain × 1 NiV S2B10 Fab Light Chain × 1 NiV S1E2 Fab Heavy Chain × 1 NiV S1E2 Fab Light Chain × 1 NIV LN3D3 Fab Heavy Chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GLYCP_NIPAV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain G； PDBConstruct 1–426； UniProt 177–602

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9lue
Deposition date deposition_date	2025-02-08
Structure title title	Cryo-EM structure of the Nipah G head domain in complex with three Fabs
Keywords keywords	Nipah G protein, Antibodies, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9lue__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9lue__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9lue__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	36.73 Å
Rg (electron density)	36.41 Å
Total Rg	36.82 Å
Atom count	8693
Residues	1099
Excluded volume	153880 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9lue__assembly_1__model_1`	heptameric （7）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Glycoprotein G
Molecular weight formula_weight	47766.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G
Atom count atom_count	8693

GVSNLVGLPNNICLQKTSNQILKPKLISYTLPVVGQSGTCITDPLLAMDEGYFAYSHLERIGSCSRGVSKQRIIGVGEVLDRGDEVPSLFMTNVWTPPNPNTVYHCSAVYNNEFYYVLCAVSTVGDPILNSTYWSGSLMMTRLAVKPKSNGGGYNQHQLALRSIEKGRYDKVMPYGPSGIKQGDTLYFPAVGFLVRTEFKYNDSNCPITKCQYSKPENCRLSMGIRPNSHYILRSGLLKYNLSDGENPKVVFIEISDQRLSIGSPSKIYDSLGQPVFYQASFSWDTMIKFGDVLTVNPLVVNWRNNTVISRPGQSQCPRFNTCPEICWEGVYNDAFLIDRINWISAGVFLDSNQTAENPVFTVFKDNEILYRAQLASEDTNAQKTITNCFLLKNKIWCISLVEIYDTGDNVIRPKLFAVKIPEQCT

Source Source

Source organism organism	Henipavirus nipahense
NCBI taxonomy ID ncbi_taxonomy_id	3052225
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	NIV LN3D3 Fab Light Chain
Molecular weight formula_weight	11782.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

EIQMTQSPATLSVTPGDSVSLSCRASQSISNNLHWYQQKSHESPRLLIKYASQSISGIPSRFSGSGSGTDFTLSINNLETEDFGMYFCQHSDSWPFTFGSGTKLEIK

Source Source

Source organism organism	Mesocricetus auratus
NCBI taxonomy ID ncbi_taxonomy_id	10036
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	NiV S2B10 Fab Heavy Chain
Molecular weight formula_weight	13474.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

QMQLQESGPGLVKPSQSLSLTCTVTGYSITSDYAWNWIRQFPRNKLEWMGFITYSGSTSYNPSLKSRISLTRDTSKNQFFLQLSSVTTEDTATYYCARSGANWDWFAYWGQGTLVTVSA

Source Source

Source organism organism	Mesocricetus auratus
NCBI taxonomy ID ncbi_taxonomy_id	10036
Host organism host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	NiV S2B10 Fab Light Chain
Molecular weight formula_weight	12196.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DIQMTQSPASLAVSLGQRATISCRASESVDNYGNSFMHWYQQKPGQPPKLLIYRASKLESGIPARFSGSGSRTDFTLTINPVEADDVATYHCQQSNEDPWTFGGGTKLEIK

Source Source

Source organism organism	Mesocricetus auratus
NCBI taxonomy ID ncbi_taxonomy_id	10036
Host organism host_organism	Homo sapiens

Entity 5 Entity 5 polymer

Description description	NiV S1E2 Fab Heavy Chain
Molecular weight formula_weight	13737.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

QMQLQESGPGLVKPSQSLSLTCSVTGYSITSGYYWNWIRQFSGNKLEWMGYINHDGSKNYNPSLKNRISITRDTSKNQFFLKLNSVTTEDTATYYCARDYGSYYYPMDYWGQGTSVTVSS

Source Source

Source organism organism	Mesocricetus auratus
NCBI taxonomy ID ncbi_taxonomy_id	10036
Host organism host_organism	Homo sapiens

Entity 6 Entity 6 polymer

Description description	NiV S1E2 Fab Light Chain
Molecular weight formula_weight	11425.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

EIVLTQSPPIMSASPGEKVTITCSASSSVTFMHWFQQKPGTSPKLWIFSTSNLASGVPARFSGSGSGTSYSLTISRMEAEDAATYYCQQRSSYPFTFGSGTKLEIK

Source Source

Source organism organism	Mesocricetus auratus
NCBI taxonomy ID ncbi_taxonomy_id	10036
Host organism host_organism	Homo sapiens

Entity 7 Entity 7 polymer

Description description	NIV LN3D3 Fab Heavy Chain
Molecular weight formula_weight	13380.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

EVKLEESGPELVKPGASVKMSCKASGYTFTNYVMHWVKQKPGQGLEWIGYVNPYNDGTQYNEKFRDKATLTSDKSSSTVYMELNSLTSEDSAVYYCTRGDYPYWVFEVWGAGTTVTVSS

Source Source

Source organism organism	Mesocricetus auratus
NCBI taxonomy ID ncbi_taxonomy_id	10036
Host organism host_organism	Homo sapiens

Entity 8 Entity 8 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	5

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.030 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.03 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	145635

Cryo-EM structure of the Nipah G head domain in complex with three Fabs

1. Protein Identity and Related Structures Protein Identity & Related Structures

Glycoprotein G

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9lue__assembly_1__model_1

9lue__assembly_1__model_1 | I(q)

9lue__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

Entity 8 Entity 8 non-polymer

7. Citations (1)

Cryo-EM structure of the Nipah G head domain in complex with three Fabs

1. Protein Identity and Related Structures Protein Identity & Related Structures

Glycoprotein G

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9lue__assembly_1__model_1

9lue__assembly_1__model_1 | I(q)

9lue__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

Entity 8 Entity 8 non-polymer

7. Citations (1)