6P7S: Attachment glycoprotein

Crystal Structure of the Cedar henipavirus Attachment G Glycoprotein globular domain in complex with the receptor ephrin-B1. Determined by X-ray diffraction at 3.49 Å resolution. Released 25 Sept 2019.

Method: X-ray diffraction
Resolution: 3.49 Å
Organisms: Cedar virus, Mus musculus
Chains: 4
Atoms: 9,114
Mol. weight: 133.78 kDa
Ligands: NAG
Released: 25 Sept 2019

Explore 6P7S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6P7S contains 21 α-helices and 91 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: 5 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	224-226	3	1
β-strand	238-248	11	2
β-strand	251-260	10	2
β-strand	270-280	11	2
β-strand	286-295	10	2
α-helix	299-301	3
β-strand	302-310	9	3
β-strand	313-320	8	3
β-strand	336-342	7	3
β-strand	349-352	4	3
α-helix	353	1
β-strand	359-360	2	4
β-strand	366-369	4	4
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	444-451	8	4
β-strand	452	1	5
α-helix	453	1
β-strand	463-468	6	6
β-strand	471-476	6	6
β-strand	482	1	7
β-strand	487-492	6	6
β-strand	496	1	5
β-strand	497-500	4	6
β-strand	519	1	7
β-strand	526	1	8
β-strand	530	1	1
β-strand	532-534	3	9
β-strand	542-547	6	9
β-strand	554	1	1
β-strand	556-561	6	9
β-strand	566-571	6	9
β-strand	578-588	11	1
β-strand	593-602	10	1
β-strand	609	1	2
β-strand	612-617	6	1

Chain B: 5 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	31	1	10
α-helix	32-34	3
β-strand	35-36	2	10
β-strand	45	1	11
β-strand	49	1	11
β-strand	50-52	3	12
α-helix	54-55	2
β-strand	59-64	6	10
α-helix	65-68	4
β-strand	76-81	6	12
α-helix	83-88	6
β-strand	90	1	13
β-strand	96-101	6	12
β-strand	108-113	6	10
β-strand	120	1	8
β-strand	131-135	5	12
β-strand	149	1	13
α-helix	152-155	4
β-strand	159-163	5	12

Chain C: 5 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	224-226	3	14
β-strand	238-248	11	15
β-strand	251-260	10	15
β-strand	270-280	11	15
β-strand	286-295	10	15
α-helix	299-301	3
β-strand	302-310	9	16
β-strand	313-320	8	16
β-strand	336-342	7	16
β-strand	349-352	4	16
α-helix	353	1
β-strand	359-360	2	17
β-strand	366-369	4	17
β-strand	375-377	3	17
β-strand	380-389	10	17
α-helix	397-400	4
α-helix	412-418	7
β-strand	421	1	17
β-strand	429-440	12	17
β-strand	444-451	8	17
β-strand	452	1	18
α-helix	453	1
β-strand	463-468	6	19
β-strand	471-476	6	19
β-strand	486-489	4	19
β-strand	490-492	3	20
β-strand	496	1	18
β-strand	497-498	2	20
β-strand	530	1	14
β-strand	532-534	3	21
β-strand	542-547	6	21
β-strand	554	1	14
β-strand	556-561	6	21
β-strand	566-571	6	21
β-strand	578-588	11	14
β-strand	593-602	10	14
β-strand	612-617	6	14

Chain D: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	31-34	4
β-strand	35-36	2	22
β-strand	50-52	3	23
α-helix	54-55	2
β-strand	61-64	4	22
α-helix	65-68	4
α-helix	71-73	3
β-strand	76-81	6	23
α-helix	83-88	6
β-strand	90	1	24
β-strand	97-101	5	23
β-strand	108-111	4	22
β-strand	131-136	6	23
β-strand	149	1	24
α-helix	151-153	3
β-strand	159-163	5	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Attachment glycoprotein	A, C	protein	429	Cedar virus	J7H333 (AlphaFold model)
Ephrin-B1	B, D	protein	142	Mus musculus	P52795 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6P7S_1 Attachment glycoprotein (chains A, C)
AMYSTNAYAELAGPPKIFCKSVSKDPDFRLKQIDYVIPVQQDRSICMNNPLLDISDGFFT
YIHYEGINSCKKSDSFKVLLSHGEIVDRGDYRPSLYLLSSHYHPYSMQVINCVPVTCNQS
SFVFCHISNNTKTLDNSDYSSDEYYITYFNGIDRPKTKKIPINNMTADNRYIHFTFSGGG
GVCLGEEFIIPVTTVINTDVFTHDYCESFNCSVQTGKSLKEICSESLRSPTNSSRYNLNG
IMIISQNNMTDFKIQLNGITYNKLSFGSPGRLSKTLGQVLYYQSSMSWDTYLKAGFVEKW
KPFTPNWMNNTVISRPNQGNCPRYHKCPEICYGGTYNDIAPLDLGKDMYVSVILDSDQLA
ENPEITVFNSTTILYKERVSKDELNTRSTTTSCFLFLDEPWCISVLETNRFNGKSIRPEI
YSYKIPKYC

Sequence of entity 2 (B, D), FASTA

>6P7S_2 Ephrin-B1 (chains B, D)
AKNLEPVSWSSLNPKFLSGKGLVIYPKIGDKLDIICPRAEAGRPYEYYKLYLVRPEQAAA
CSTVLDPNVLVTCNKPHQEIRFTIKFQEFSPNYMGLEFKKYHDYYITSTSNGSLEGLENR
EGGVCRTRTMKIVMKVGQDPNA

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	8

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)
6P7Y 2.84 Å, Crystal Structure of the Cedar henipavirus Attachment G Glycoprotein globular domain in…
6P72 3.28 Å, Crystal Structure of the Cedar henipavirus Attachment G Glycoprotein global domain
6THG 4.07 Å, Cedar Virus attachment glycoprotein (G) in complex with human ephrin-B1

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