6THG: Cedar Virus attachment glycoprotein

Cedar Virus attachment glycoprotein (G) in complex with human ephrin-B1. Determined by X-ray diffraction at 4.07 Å resolution. Released 18 Dec 2019.

Method: X-ray diffraction
Resolution: 4.07 Å
Organisms: Cedar virus, Homo sapiens
Chains: 10
Atoms: 22,772
Mol. weight: 340.6 kDa
Ligands: NAG
Released: 18 Dec 2019

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

Secondary structure: helices and β-sheets

6THG contains 70 α-helices and 212 β-strands across 10 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	224-226	3	11
β-strand	238-248	11	12
β-strand	251-260	10	12
β-strand	270-280	11	12
β-strand	286-295	10	12
α-helix	299-301	3
β-strand	302-310	9	13
β-strand	313-320	8	13
α-helix	326-329	4
α-helix	332-334	3
β-strand	336-342	7	13
α-helix	347-348	2
β-strand	349-352	4	13
α-helix	355-357	3
β-strand	358-360	3	14
β-strand	366-369	4	14
β-strand	371	1	15
β-strand	375-377	3	14
β-strand	380-389	10	14
α-helix	397-400	4
α-helix	405-407	3
α-helix	412-418	7
β-strand	421	1	14
β-strand	429-438	10	14
β-strand	446-451	6	14
β-strand	452	1	16
α-helix	453	1
β-strand	463-468	6	15
β-strand	471-476	6	15
β-strand	486-489	4	15
β-strand	490-492	3	17
β-strand	496	1	16
β-strand	497-498	2	17
β-strand	530	1	11
β-strand	532-536	5	18
β-strand	541-547	7	18
β-strand	554	1	11
β-strand	556-561	6	18
β-strand	566-571	6	18
β-strand	578-589	12	11
β-strand	592-602	11	11
β-strand	612-617	6	11

Chain B: 9 helices, 33 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
α-helix	326-329	4
α-helix	332-334	3
β-strand	336-342	7	3
α-helix	346-348	3
β-strand	349-352	4	3
α-helix	355-357	3
β-strand	358-360	3	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	405-407	3
α-helix	412-418	7
β-strand	421	1	4
β-strand	429-438	10	4
β-strand	446-451	6	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	529-530	2	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	609	1	2
β-strand	612-617	6	1

Chains C, D and F: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	45	1	42
β-strand	49	1	42
β-strand	50-52	3	43
α-helix	54-55	2
β-strand	59-61	3	44
α-helix	63-65	3
β-strand	77-81	5	43
α-helix	83-88	6
β-strand	97-100	4	43
β-strand	111-113	3	44
β-strand	131-136	6	43
α-helix	142-144	3
α-helix	152-155	4
β-strand	160-163	4	43

Chain E: 9 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	224-226	3	19
β-strand	238-248	11	20
β-strand	251-260	10	20
β-strand	270-280	11	20
β-strand	286-295	10	20
α-helix	299-301	3
β-strand	302-310	9	21
β-strand	313-320	8	21
α-helix	326-329	4
α-helix	332-334	3
β-strand	336-342	7	21
α-helix	347-348	2
β-strand	349-352	4	21
α-helix	355-357	3
β-strand	358-360	3	22
β-strand	366-369	4	22
β-strand	371	1	23
β-strand	375-377	3	22
β-strand	380-389	10	22
α-helix	397-400	4
α-helix	405-407	3
α-helix	412-418	7
β-strand	421	1	22
β-strand	429-438	10	22
β-strand	446-451	6	22
β-strand	452	1	24
α-helix	453	1
β-strand	463-468	6	23
β-strand	471-476	6	23
β-strand	486-489	4	23
β-strand	490-492	3	25
β-strand	496	1	24
β-strand	497-498	2	25
β-strand	530	1	19
β-strand	533-536	4	26
β-strand	541-547	7	26
β-strand	554	1	19
β-strand	556-561	6	26
β-strand	566-571	6	26
β-strand	578-589	12	19
β-strand	592-602	11	19
β-strand	609	1	20
β-strand	612-617	6	19

Chain G: 9 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	224-226	3	27
β-strand	238-248	11	28
β-strand	251-260	10	28
β-strand	270-280	11	28
β-strand	286-295	10	28
α-helix	299-301	3
β-strand	302-310	9	29
β-strand	313-320	8	29
α-helix	326-329	4
α-helix	332-334	3
β-strand	336-342	7	29
α-helix	347-348	2
β-strand	349-352	4	29
α-helix	355-357	3
β-strand	358-360	3	30
β-strand	366-369	4	30
β-strand	371	1	31
β-strand	375-377	3	30
β-strand	380-389	10	30
α-helix	397-400	4
α-helix	405-407	3
α-helix	412-418	7
β-strand	421	1	30
β-strand	429-438	10	30
β-strand	446-451	6	30
β-strand	452	1	32
α-helix	453	1
β-strand	463-468	6	31
β-strand	471-476	6	31
β-strand	486-492	7	31
β-strand	496	1	32
β-strand	497-500	4	31
β-strand	529-530	2	27
β-strand	532-536	5	33
β-strand	541-547	7	33
β-strand	554	1	27
β-strand	556-561	6	33
β-strand	566-571	6	33
β-strand	578-589	12	27
β-strand	592-602	11	27
β-strand	609	1	28
β-strand	612-617	6	27

Chain H: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	45	1	48
β-strand	49	1	48
β-strand	50-52	3	49
α-helix	54-55	2
β-strand	59-61	3	50
α-helix	63-65	3
β-strand	77-81	5	49
α-helix	83-88	6
β-strand	96-100	5	49
β-strand	111-113	3	50
β-strand	131-136	6	49
α-helix	142-144	3
α-helix	152-155	4
β-strand	160-163	4	49

Chain I: 9 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	224-226	3	34
β-strand	238-248	11	35
β-strand	251-260	10	35
β-strand	270-280	11	35
β-strand	286-295	10	35
α-helix	299-301	3
β-strand	302-310	9	36
β-strand	313-320	8	36
α-helix	326-329	4
α-helix	332-334	3
β-strand	336-342	7	36
α-helix	347-348	2
β-strand	349-352	4	36
α-helix	355-357	3
β-strand	358-360	3	37
β-strand	366-369	4	37
β-strand	371	1	38
β-strand	375-377	3	37
β-strand	380-389	10	37
α-helix	397-400	4
α-helix	405-407	3
α-helix	412-418	7
β-strand	421-422	2	37
β-strand	425-438	14	37
β-strand	446-451	6	37
β-strand	452	1	39
α-helix	453	1
β-strand	463-468	6	38
β-strand	471-476	6	38
β-strand	486-492	7	38
β-strand	496	1	39
β-strand	497-500	4	38
β-strand	529-530	2	34
β-strand	533-536	4	40
β-strand	541-547	7	40
β-strand	554	1	41
β-strand	556-561	6	40
β-strand	566-571	6	40
β-strand	578	1	41
β-strand	579-589	11	34
β-strand	592-601	10	34
β-strand	609	1	35
β-strand	612-617	6	34

Chain J: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	45	1	51
β-strand	49	1	51
β-strand	50-52	3	52
α-helix	54-55	2
β-strand	59-61	3	53
α-helix	63-65	3
β-strand	77-81	5	52
α-helix	83-88	6
β-strand	97-100	4	52
β-strand	111-113	3	53
β-strand	131-136	6	52
α-helix	142-144	3
α-helix	152-155	4
β-strand	159-163	5	52

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Attachment glycoprotein	A, B, E, G, I	protein	426	Cedar virus	J7H333 (AlphaFold model)
Ephrin-B1	C, D, F, H, J	protein	151	Homo sapiens	P98172 (AlphaFold model)

Sequence of entity 1 (A, B, E, G, I), FASTA

>6THG_1 Attachment glycoprotein (chains A, B, E, G, I)
ETGKIFCKSVSKDPDFRLKQIDYVIPVQQDRSICMNNPLLDISDGFFTYIHYEGINSCKK
SDSFKVLLSHGEIVDRGDYRPSLYLLSSHYHPYSMQVINCVPVTCNQSSFVFCHISNNTK
TLDNSDYSSDEYYITYFNGIDRPKTKKIPINNMTADNRYIHFTFSGGGGVCLGEEFIIPV
TTVINTDVFTHDYCESFNCSVQTGKSLKEICSESLRSPTNSSRYNLNGIMIISQNNMTDF
KIQLNGITYNKLSFGSPGRLSKTLGQVLYYQSSMSWDTYLKAGFVEKWKPFTPNWMNNTV
ISRPNQGNCPRYHKCPEICYGGTYNDIAPLDLGKDMYVSVILDSDQLAENPEITVFNSTT
ILYKERVSKDELNTRSTTTSCFLFLDEPWCISVLETNRFNGKSIRPEIYSYKIPKYCGTK
HHHHHH

Sequence of entity 2 (C, D, F, H, J), FASTA

>6THG_2 Ephrin-B1 (chains C, D, F, H, J)
ETGAKNLEPVSWSSLNPKFLSGKGLVIYPKIGDKLDIICPRAEAGRPYEYYKLYLVRPEQ
AAACSTVLDPNVLVTCNRPEQEIRFTIKFQEFSPNYMGLEFKKHHDYYITSTSNGSLEGL
ENREGGVCRTRTMKIIMKVGQDGTKHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	17

Primary citation

A key region of molecular specificity orchestrates unique ephrin-B1 utilization by Cedar virus. Pryce, R., Azarm, K., Rissanen, I. et al. Life Sci Alliance (2020) 3. DOI 10.26508/lsa.201900578 · 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
6P7S 3.49 Å, Crystal Structure of the Cedar henipavirus Attachment G Glycoprotein globular domain in…

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