6P7Y: Attachment glycoprotein

Crystal Structure of the Cedar henipavirus Attachment G Glycoprotein globular domain in complex with the receptor ephrin-B2. Determined by X-ray diffraction at 2.84 Å resolution. Released 25 Sept 2019.

Method: X-ray diffraction
Resolution: 2.84 Å
Organisms: Cedar virus, Homo sapiens
Chains: 4
Atoms: 9,852
Mol. weight: 140.07 kDa
Ligands: NAG
Released: 25 Sept 2019

Explore 6P7Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6P7Y contains 25 α-helices and 92 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 9 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	201-203	3	1
β-strand	224-226	3	1
β-strand	238-248	11	2
β-strand	251-260	10	2
α-helix	265-267	3
β-strand	268-280	13	2
β-strand	286-295	10	2
α-helix	299-301	3
β-strand	302-310	9	3
β-strand	313-320	8	3
α-helix	326-329	4
α-helix	332-334	3
β-strand	336-342	7	3
α-helix	347-348	2
β-strand	349-352	4	3
α-helix	355-357	3
β-strand	359-360	2	4
β-strand	366-369	4	4
β-strand	371	1	5
β-strand	375-377	3	4
β-strand	380-389	10	4
α-helix	397-400	4
α-helix	412-418	7
β-strand	421	1	4
β-strand	429-440	12	4
β-strand	443-451	9	4
β-strand	452	1	6
α-helix	453	1
β-strand	463-468	6	5
β-strand	471-476	6	5
β-strand	486-492	7	5
β-strand	496	1	6
β-strand	497-500	4	5
β-strand	530	1	1
β-strand	532-536	5	7
β-strand	541-547	7	7
β-strand	554	1	1
β-strand	556-561	6	7
β-strand	566-571	6	7
β-strand	578-589	12	1
β-strand	592-602	11	1
β-strand	612-617	6	1

Chain B: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	29	1	8
α-helix	30-32	3
β-strand	33-34	2	8
α-helix	43	1
β-strand	48-50	3	9
β-strand	57-62	6	8
β-strand	76-78	3	10
β-strand	79-81	3	9
α-helix	83-88	6
β-strand	90	1	11
β-strand	99-101	3	10
β-strand	108-113	6	8
β-strand	130-135	6	9
α-helix	142-144	3
β-strand	149	1	11
α-helix	151-154	4
β-strand	159-164	6	9

Chain C: 8 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	201-202	2	12
β-strand	224-226	3	12
β-strand	238-248	11	13
β-strand	251-260	10	13
β-strand	270-280	11	13
β-strand	286-295	10	13
α-helix	299-301	3
β-strand	302-310	9	14
β-strand	313-320	8	14
α-helix	326-329	4
α-helix	332-334	3
β-strand	336-342	7	14
α-helix	347-348	2
β-strand	349-352	4	14
α-helix	355-357	3
β-strand	359-360	2	15
β-strand	366-369	4	15
β-strand	371-373	3	16
β-strand	375-377	3	15
β-strand	380-389	10	15
α-helix	397-400	4
α-helix	412-418	7
β-strand	421	1	15
β-strand	429-440	12	15
β-strand	443-451	9	15
β-strand	452	1	17
α-helix	453	1
β-strand	463-468	6	16
β-strand	471-476	6	16
β-strand	486-492	7	16
β-strand	496	1	17
β-strand	497-500	4	16
β-strand	530	1	12
β-strand	533-536	4	18
β-strand	541-547	7	18
β-strand	554	1	12
β-strand	556-561	6	18
β-strand	566-571	6	18
β-strand	578-589	12	12
β-strand	592-602	11	12
β-strand	612-617	6	12

Chain D: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	29	1	19
α-helix	30-32	3
β-strand	33-34	2	19
β-strand	48-50	3	20
β-strand	57-62	6	19
β-strand	75	1	21
β-strand	76-78	3	22
β-strand	79-81	3	20
α-helix	83-88	6
β-strand	90	1	23
β-strand	99-101	3	22
β-strand	108-113	6	19
β-strand	130-135	6	20
β-strand	140	1	21
β-strand	149	1	23
α-helix	151-154	4
β-strand	160-164	5	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Attachment glycoprotein	A, C	protein	430	Cedar virus	J7H333 (AlphaFold model)
Ephrin-B2	B, D	protein	144	Homo sapiens	P52799 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6P7Y_1 Attachment glycoprotein (chains A, C)
SAMYSTNAYAELAGPPKIFCKSVSKDPDFRLKQIDYVIPVQQDRSICMNNPLLDISDGFF
TYIHYEGINSCKKSDSFKVLLSHGEIVDRGDYRPSLYLLSSHYHPYSMQVINCVPVTCNQ
SSFVFCHISNNTKTLDNSDYSSDEYYITYFNGIDRPKTKKIPINNMTADNRYIHFTFSGG
GGVCLGEEFIIPVTTVINTDVFTHDYCESFNCSVQTGKSLKEICSESLRSPTNSSRYNLN
GIMIISQNNMTDFKIQLNGITYNKLSFGSPGRLSKTLGQVLYYQSSMSWDTYLKAGFVEK
WKPFTPNWMNNTVISRPNQGNCPRYHKCPEICYGGTYNDIAPLDLGKDMYVSVILDSDQL
AENPEITVFNSTTILYKERVSKDELNTRSTTTSCFLFLDEPWCISVLETNRFNGKSIRPE
IYSYKIPKYC

Sequence of entity 2 (B, D), FASTA

>6P7Y_2 Ephrin-B2 (chains B, D)
SIVLEPIYWQSSNSKFLPGQGLVLYPQIGDKLDIICPKVDSKTVGQYEYYKVYMVDKDQA
DRCTIKKENTPLLNCAKPDQDIKFTIKFQEFSPNLWGLEFQKNKDYYIISTSNGSLEGLD
NQEGGVCQTRAMKILMKVGQDASS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

Structural and functional analyses reveal promiscuous and species specific use of ephrin receptors by Cedar virus. Laing, E.D., Navaratnarajah, C.K., Cheliout Da Silva, S. et al. Proc Natl Acad Sci U S A (2019) 116:20707-20715. DOI 10.1073/pnas.1911773116 · PubMed

Other PDB entries of the same protein (UniProt J7H333 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6THB 2.78 Å, Receptor binding domain of the Cedar Virus attachment glycoprotein (G)
6P72 3.28 Å, Crystal Structure of the Cedar henipavirus Attachment G Glycoprotein global domain
6P7S 3.49 Å, Crystal Structure of the Cedar henipavirus Attachment G Glycoprotein globular domain in…
6THG 4.07 Å, Cedar Virus attachment glycoprotein (G) in complex with human ephrin-B1

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