3d12

Crystal Structures of Nipah Virus G Attachment Glycoprotein in Complex with its Receptor Ephrin-B3

Method: X-RAY DIFFRACTION

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

Hemagglutinin-neuraminidase

Nipah virus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 4 其他Polymer 6	Ephrin-B3 × 2 （O35393） ;beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;beta-D-glucopyranose-(1-3)-[alpha-D-glucopyranose-(1-6)]beta-D-gulopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[beta-D-glucopyranose-(1-3)][alpha-D-glucopyranose-(1-6)]2-acetamido-2-deoxy-alpha-D-idopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;beta-D-glucopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;beta-D-glucopyranose-(1-3)-[alpha-D-glucopyranose-(1-6)]beta-D-gulopyranose-(1-4)-2-acetamido-2-deoxy-alpha-L-glucopyranose-(1-4)-[beta-D-glucopyranose-(1-3)][alpha-L-galactopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-gulopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SULFATE ION × 22 water × 4	Consistent with protein count
2	Other combination	Heteromer	Protein 2 其他Polymer 3	Ephrin-B3 × 1 （O35393） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;beta-D-glucopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;beta-D-glucopyranose-(1-3)-[alpha-D-glucopyranose-(1-6)]beta-D-gulopyranose-(1-4)-2-acetamido-2-deoxy-alpha-L-glucopyranose-(1-4)-[beta-D-glucopyranose-(1-3)][alpha-L-galactopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-gulopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SULFATE ION × 11 water × 2	Consistent with protein count
3	Other combination	Heteromer	Protein 2 其他Polymer 3	Ephrin-B3 × 1 （O35393） ;beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;beta-D-glucopyranose-(1-3)-[alpha-D-glucopyranose-(1-6)]beta-D-gulopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[beta-D-glucopyranose-(1-3)][alpha-D-glucopyranose-(1-6)]2-acetamido-2-deoxy-alpha-D-idopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SULFATE ION × 11 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HN_NIPAV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–427； UniProt 176–602 Author chain D； PDBConstruct 1–427； UniProt 176–602

Ephrin-B3

Mus musculus

UniProt O35393

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 4 其他Polymer 6	Hemagglutinin-neuraminidase × 2 （Q9IH62） ;beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;beta-D-glucopyranose-(1-3)-[alpha-D-glucopyranose-(1-6)]beta-D-gulopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[beta-D-glucopyranose-(1-3)][alpha-D-glucopyranose-(1-6)]2-acetamido-2-deoxy-alpha-D-idopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;beta-D-glucopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;beta-D-glucopyranose-(1-3)-[alpha-D-glucopyranose-(1-6)]beta-D-gulopyranose-(1-4)-2-acetamido-2-deoxy-alpha-L-glucopyranose-(1-4)-[beta-D-glucopyranose-(1-3)][alpha-L-galactopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-gulopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SULFATE ION × 22 water × 4	Consistent with protein count
2	Other combination	Heteromer	Protein 2 其他Polymer 3	Hemagglutinin-neuraminidase × 1 （Q9IH62） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;beta-D-glucopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;beta-D-glucopyranose-(1-3)-[alpha-D-glucopyranose-(1-6)]beta-D-gulopyranose-(1-4)-2-acetamido-2-deoxy-alpha-L-glucopyranose-(1-4)-[beta-D-glucopyranose-(1-3)][alpha-L-galactopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-gulopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SULFATE ION × 11 water × 2	Consistent with protein count
3	Other combination	Heteromer	Protein 2 其他Polymer 3	Hemagglutinin-neuraminidase × 1 （Q9IH62） ;beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;beta-D-glucopyranose-(1-3)-[alpha-D-glucopyranose-(1-6)]beta-D-gulopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[beta-D-glucopyranose-(1-3)][alpha-D-glucopyranose-(1-6)]2-acetamido-2-deoxy-alpha-D-idopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SULFATE ION × 11 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EFNB3_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–141； UniProt 29–169 Author chain E； PDBConstruct 1–141； UniProt 29–169

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	3d12
Deposition date deposition_date	2008-05-02
Structure title title	Crystal Structures of Nipah Virus G Attachment Glycoprotein in Complex with its Receptor Ephrin-B3
Keywords keywords	;Beta propeller, Protein-Receptor complex, Envelope protein, Glycoprotein, Hemagglutinin, Hydrolase, Membrane, Signal-anchor, Transmembrane, Virion, Developmental protein, Differentiation, Neurogenesis, HYDROLASE-MEMBRANE PROTEIN COMPLEX ;; HYDROLASE/MEMBRANE PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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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.

3d12__assembly_1__model_1

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

Download this curve (.dat)

3d12__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3d12__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.05 Å
Rg (electron density)	36.90 Å
Total Rg	37.34 Å
Atom count	9486
Residues	1138
Excluded volume	168210 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3d12__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3d12__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3d12__assembly_3__model_1`	dimeric （2）	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 (10)

Entity 1 Entity 1 polymer

Description description	Hemagglutinin-neuraminidase
Molecular weight formula_weight	47966.5 kDa
EC 编号 ec_number	3.2.1.18
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	9598

EGVSNLVGLPNNICLQKTSNQILKPKLISYTLPVVGQSGTCITDPLLAMDEGYFAYSHLERIGSCSRGVSKQRIIGVGEVLDRGDEVPSLFMTNVWTPPNPNTVYHCSAVYNNEFYYVLCAVSTVGDPILNSTYWSGSLMMTRLAVKPKSNGGGYNQHQLALRSIEKGRYDKVMPYGPSGIKQGDTLYFPAVGFLVRTEFKYNDSNCPITKCQYSKPENCRLSMGIRPNSHYILRSGLLKYNLSDGENPKVVFIEISDQRLSIGSPSKIYDSLGQPVFYQASFSWDTMIKFGDVLTVNPLVVNWRNNTVISRPGQSQCPRFNTCPEICWEGVYNDAFLIDRINWISAGVFLDSNQTAENPVFTVFKDNEILYRAQLASEDTNAQKTITNCFLLKNKIWCISLVEIYDTGDNVIRPKLFAVKIPEQCTA

Source Source

Source organism organism	Nipah virus
NCBI taxonomy ID ncbi_taxonomy_id	121791
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Ephrin-B3
Molecular weight formula_weight	16065.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

SLEPVYWNSANKRFQAEGGYVLYPQIGDRLDLLCPRARPPGPHSSPSYEFYKLYLVEGAQGRRCEAPPAPNLLLTCDRPDLDLRFTIKFQEYSPNLWGHEFRSHHDYYIIATSDGTREGLESLQGGVCLTRGMKVLLRVGQ

Source Source

Source organism organism	Mus musculus
Common name common_name	mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Spodoptera frugiperda

Entity 3 Entity 3 branched

Description description	;beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	910.8 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 branched

Description description	;beta-D-glucopyranose-(1-3)-[alpha-D-glucopyranose-(1-6)]beta-D-gulopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[beta-D-glucopyranose-(1-3)][alpha-D-glucopyranose-(1-6)]2-acetamido-2-deoxy-alpha-D-idopyranose ;
Molecular weight formula_weight	1235.1 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	2

Entity 6 Entity 6 branched

Description description	;beta-D-glucopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	910.8 kDa
Source method src_method	man
Copy count entity_count	1

Entity 7 Entity 7 branched

Description description	;beta-D-glucopyranose-(1-3)-[alpha-D-glucopyranose-(1-6)]beta-D-gulopyranose-(1-4)-2-acetamido-2-deoxy-alpha-L-glucopyranose-(1-4)-[beta-D-glucopyranose-(1-3)][alpha-L-galactopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-gulopyranose ;
Molecular weight formula_weight	1235.1 kDa
Source method src_method	man
Copy count entity_count	1

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	man
Copy count entity_count	2

Entity 9 Entity 9 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	22

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	112

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3d12b_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.0 — automated matches

Domain ID domain_id	d3d12e_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	3d12A00
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3d12B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3d12D00
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3d12E00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

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Unit-cell length a length_a	189.492 Å
Unit-cell length b length_b	189.492 Å
Unit-cell length c length_c	277.052 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	3.005 Å
Low-resolution limit resolution_low	39.337 Å
R factor r_factor	—
R_work r_work	0.2210
R_free r_free	0.2650

Crystal Structures of Nipah Virus G Attachment Glycoprotein in Complex with its Receptor Ephrin-B3

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

Hemagglutinin-neuraminidase

State in the Current Structure

Other States of the Same Protein in the Database

Ephrin-B3

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

3d12__assembly_1__model_1

3d12__assembly_1__model_1 | I(q)

3d12__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 branched

Entity 7 Entity 7 branched

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structures of Nipah Virus G Attachment Glycoprotein in Complex with its Receptor Ephrin-B3

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

Hemagglutinin-neuraminidase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ephrin-B3

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

3d12__assembly_1__model_1

3d12__assembly_1__model_1 | I(q)

3d12__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 branched

Entity 7 Entity 7 branched

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)