6p7y

Crystal Structure of the Cedar henipavirus Attachment G Glycoprotein globular domain in complex with the receptor ephrin-B2

Method: X-RAY DIFFRACTION

▼

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

Attachment glycoprotein

Cedar virus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 2 其他Polymer 6	Ephrin-B2 × 1 （P52799） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 ; × 1 ;alpha-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 ; × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 2	Consistent with protein count
2	Other combination	Heteromer	Protein 2 其他Polymer 5	Ephrin-B2 × 1 （P52799） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-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 ; × 2 ;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 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	J7H333_9MONO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–430； UniProt 193–622 Author chain C； PDBConstruct 1–430； UniProt 193–622

Ephrin-B2

Homo sapiens

UniProt P52799

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 2 其他Polymer 6	Attachment glycoprotein × 1 （J7H333） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 ; × 1 ;alpha-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 ; × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 2	Consistent with protein count
2	Other combination	Heteromer	Protein 2 其他Polymer 5	Attachment glycoprotein × 1 （J7H333） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-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 ; × 2 ;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 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EFNB2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–144； UniProt 27–170 Author chain D； PDBConstruct 1–144； UniProt 27–170

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6p7y
Deposition date deposition_date	2019-06-06
Structure title title	Crystal Structure of the Cedar henipavirus Attachment G Glycoprotein globular domain in complex with the receptor ephrin-B2
Keywords keywords	Cedar virus, attachment, glycoprotein, G protein, VIRAL PROTEIN, receptor, ephrin-B2, henipavirus; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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.

6p7y__assembly_1__model_1

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

Download this curve (.dat)

6p7y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6p7y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.88 Å
Rg (electron density)	24.83 Å
Total Rg	25.90 Å
Atom count	4894
Residues	567
Excluded volume	87290 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6p7y__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6p7y__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	Attachment glycoprotein
Molecular weight formula_weight	49042.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	9852

SAMYSTNAYAELAGPPKIFCKSVSKDPDFRLKQIDYVIPVQQDRSICMNNPLLDISDGFFTYIHYEGINSCKKSDSFKVLLSHGEIVDRGDYRPSLYLLSSHYHPYSMQVINCVPVTCNQSSFVFCHISNNTKTLDNSDYSSDEYYITYFNGIDRPKTKKIPINNMTADNRYIHFTFSGGGGVCLGEEFIIPVTTVINTDVFTHDYCESFNCSVQTGKSLKEICSESLRSPTNSSRYNLNGIMIISQNNMTDFKIQLNGITYNKLSFGSPGRLSKTLGQVLYYQSSMSWDTYLKAGFVEKWKPFTPNWMNNTVISRPNQGNCPRYHKCPEICYGGTYNDIAPLDLGKDMYVSVILDSDQLAENPEITVFNSTTILYKERVSKDELNTRSTTTSCFLFLDEPWCISVLETNRFNGKSIRPEIYSYKIPKYC

Source Source

Source organism organism	Cedar virus
NCBI taxonomy ID ncbi_taxonomy_id	1221391
Host organism host_organism	Insect cell expression vector pTIE1

Entity 2 Entity 2 polymer

Description description	Ephrin-B2
Molecular weight formula_weight	16362.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SIVLEPIYWQSSNSKFLPGQGLVLYPQIGDKLDIICPKVDSKTVGQYEYYKVYMVDKDQADRCTIKKENTPLLNCAKPDQDIKFTIKFQEFSPNLWGLEFQKNKDYYIISTSNGSLEGLDNQEGGVCQTRAMKILMKVGQDASS

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Insect cell expression vector pTIE1

Entity 3 Entity 3 branched

Description description	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	586.5 kDa
Source method src_method	man
Copy count entity_count	2

Entity 4 Entity 4 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	570.5 kDa
Source method src_method	man
Copy count entity_count	2

Entity 5 Entity 5 branched

Description description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 ;
Molecular weight formula_weight	1203.1 kDa
Source method src_method	man
Copy count entity_count	1

Entity 6 Entity 6 branched

Description description	;alpha-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	5

Entity 7 Entity 7 branched

Description description	;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	748.7 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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	161

▼

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6p7yb_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.5 — Ephrin ectodomain

Domain ID domain_id	d6p7yd_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.5 — Ephrin ectodomain

CATH v4.4 (2 domains)

Domain ID domain_id	6p7yB00
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	6p7yD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

▶

Unit-cell length a length_a	207.021 Å
Unit-cell length b length_b	207.021 Å
Unit-cell length c length_c	120.650 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	12

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	2.844 Å
Low-resolution limit resolution_low	45.973 Å
R factor r_factor	0.2076
R_work r_work	0.2067
R_free r_free	0.2399

Crystal Structure of the Cedar henipavirus Attachment G Glycoprotein globular domain in complex with the receptor ephrin-B2

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

Attachment glycoprotein

State in the Current Structure

Other States of the Same Protein in the Database

Ephrin-B2

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

6p7y__assembly_1__model_1

6p7y__assembly_1__model_1 | I(q)

6p7y__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 (9)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of the Cedar henipavirus Attachment G Glycoprotein globular domain in complex with the receptor ephrin-B2

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

Attachment glycoprotein

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-B2

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

6p7y__assembly_1__model_1

6p7y__assembly_1__model_1 | I(q)

6p7y__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 (9)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)