6PDL: Hendra Virus Attachment G Glycoprotein

Crystal Structure of Hendra Virus Attachment G Glycoprotein in Complex with Receptor Ephrin-B2. Determined by X-ray diffraction at 2.7 Å resolution. Released 27 Nov 2019.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Hendra henipavirus, Homo sapiens
Chains: 8
Atoms: 18,707
Mol. weight: 273.22 kDa
Ligands: NAG
Released: 27 Nov 2019

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

Secondary structure: helices and β-sheets

6PDL contains 50 α-helices and 208 β-strands across 8 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: 8 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	178-179	2	1
β-strand	201-203	3	1
β-strand	215-225	11	2
β-strand	228-237	10	2
β-strand	244-257	14	2
β-strand	263-271	9	2
α-helix	276-278	3
β-strand	279-287	9	3
β-strand	290-297	8	3
α-helix	307-309	3
α-helix	310-312	3
β-strand	314-320	7	3
β-strand	332-335	4	3
β-strand	339-341	3	4
β-strand	347-350	4	4
β-strand	354	1	3
β-strand	356-358	3	4
β-strand	361-371	11	4
α-helix	372-374	3
α-helix	379-381	3
α-helix	394-397	4
β-strand	407-417	11	4
β-strand	425-430	6	4
β-strand	431	1	5
α-helix	432	1
β-strand	442-447	6	6
β-strand	450-455	6	6
β-strand	465-471	7	6
β-strand	475	1	5
β-strand	476-479	4	6
β-strand	505	1	7
β-strand	509	1	1
β-strand	511-515	5	8
β-strand	520-526	7	8
β-strand	533	1	1
β-strand	535-540	6	8
β-strand	545-550	6	8
β-strand	557-568	12	1
β-strand	571-581	11	1
β-strand	588	1	2
β-strand	589-596	8	1
α-helix	597-598	2

Chain B: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	29	1	9
α-helix	30-32	3
β-strand	33-34	2	9
β-strand	43	1	10
β-strand	47	1	10
β-strand	48-49	2	11
β-strand	57-62	6	9
β-strand	75	1	12
β-strand	76-81	6	11
α-helix	83-88	6
β-strand	90	1	13
β-strand	99-101	3	11
β-strand	108-113	6	9
β-strand	120	1	7
β-strand	130-136	7	11
β-strand	140	1	12
α-helix	142-144	3
β-strand	149	1	13
α-helix	151-156	6
β-strand	159-164	6	11

Chain C: 9 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	178-179	2	14
β-strand	201-202	2	14
β-strand	215-225	11	15
β-strand	228-237	10	15
α-helix	243	1
β-strand	244-257	14	15
β-strand	263-271	9	15
α-helix	276-278	3
β-strand	279-287	9	16
β-strand	290-297	8	16
α-helix	307-309	3
α-helix	310-312	3
β-strand	314-320	7	16
β-strand	332-335	4	16
β-strand	339-341	3	17
β-strand	347-350	4	17
β-strand	354	1	16
β-strand	356-358	3	17
β-strand	361-371	11	17
α-helix	372-374	3
α-helix	379-381	3
α-helix	394-397	4
β-strand	407-417	11	17
β-strand	425-430	6	17
β-strand	431	1	18
α-helix	432	1
β-strand	442-447	6	19
β-strand	450-455	6	19
β-strand	463	1	20
β-strand	465-471	7	19
β-strand	475	1	18
β-strand	476-479	4	19
β-strand	486	1	20
β-strand	505	1	21
β-strand	509	1	14
β-strand	511-515	5	22
β-strand	520-526	7	22
β-strand	533	1	14
β-strand	535-540	6	22
β-strand	545-550	6	22
β-strand	557-568	12	14
β-strand	571-581	11	14
β-strand	588	1	15
β-strand	589-596	8	14
α-helix	597-598	2

Chain D: 4 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	29	1	23
α-helix	30-32	3
β-strand	33-34	2	23
β-strand	43	1	24
β-strand	47	1	24
β-strand	48-50	3	25
β-strand	57-62	6	23
β-strand	75	1	26
β-strand	76-78	3	27
β-strand	79-81	3	25
α-helix	83-88	6
β-strand	90	1	28
β-strand	99-101	3	27
β-strand	108-113	6	23
β-strand	120	1	21
β-strand	130-135	6	25
β-strand	140	1	26
α-helix	142-144	3
β-strand	149	1	28
α-helix	151-156	6
β-strand	159-164	6	25

Chain E: 8 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	178-179	2	29
α-helix	185-187	3
β-strand	201-203	3	29
β-strand	215-225	11	30
β-strand	228-237	10	30
β-strand	244-257	14	30
β-strand	263-271	9	30
α-helix	276-278	3
β-strand	279-287	9	31
β-strand	290-297	8	31
α-helix	307-309	3
α-helix	310-312	3
β-strand	314-320	7	31
β-strand	332-334	3	31
β-strand	339-341	3	32
β-strand	347-350	4	32
β-strand	354	1	31
β-strand	356-358	3	32
β-strand	361-371	11	32
α-helix	372-374	3
α-helix	379-381	3
α-helix	394-397	4
β-strand	407-417	11	32
β-strand	425-430	6	32
β-strand	431	1	33
α-helix	432	1
β-strand	442-447	6	34
β-strand	450-455	6	34
β-strand	463	1	35
β-strand	465-471	7	34
β-strand	475	1	33
β-strand	476-479	4	34
β-strand	486	1	35
β-strand	505	1	36
β-strand	509	1	29
β-strand	511-515	5	37
β-strand	520-526	7	37
β-strand	533	1	29
β-strand	535-540	6	37
β-strand	545-550	6	37
β-strand	557-568	12	29
β-strand	571-581	11	29
β-strand	588	1	30
β-strand	589-596	8	29

Chain F: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	29	1	38
α-helix	30-32	3
β-strand	33-34	2	38
β-strand	43	1	39
β-strand	47	1	39
β-strand	48-49	2	40
α-helix	52-53	2
β-strand	57-62	6	38
β-strand	75	1	41
β-strand	76-81	6	40
α-helix	83-88	6
β-strand	90	1	42
β-strand	99-101	3	40
β-strand	108-113	6	38
β-strand	120	1	36
β-strand	130-136	7	40
β-strand	140	1	41
α-helix	142-144	3
β-strand	149	1	42
α-helix	152-155	4
β-strand	159-164	6	40

Chain G: 7 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	178-179	2	43
β-strand	201-203	3	43
β-strand	215-225	11	44
β-strand	228-237	10	44
β-strand	244-257	14	44
β-strand	263-271	9	44
α-helix	276-278	3
β-strand	279-287	9	45
β-strand	290-297	8	45
α-helix	307-309	3
β-strand	314-320	7	45
β-strand	332-335	4	45
β-strand	339-341	3	46
β-strand	347-350	4	46
β-strand	354	1	45
β-strand	356-358	3	46
β-strand	361-371	11	46
α-helix	372-374	3
α-helix	379-381	3
α-helix	394-397	4
β-strand	407-417	11	46
β-strand	425-430	6	46
β-strand	431	1	47
α-helix	432	1
β-strand	442-447	6	48
β-strand	450-455	6	48
β-strand	463	1	49
β-strand	465-471	7	48
β-strand	475	1	47
β-strand	476-479	4	48
β-strand	486	1	49
β-strand	505	1	50
β-strand	509	1	43
β-strand	511-515	5	51
β-strand	520-526	7	51
β-strand	533	1	43
β-strand	535-540	6	51
β-strand	545-550	6	51
β-strand	557-568	12	43
β-strand	571-581	11	43
β-strand	588	1	44
β-strand	589-596	8	43
α-helix	597-598	2

Chain H: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	29	1	52
α-helix	30-32	3
β-strand	33-34	2	52
β-strand	43	1	53
β-strand	47	1	53
β-strand	48-50	3	54
β-strand	57-62	6	52
α-helix	70-72	3
β-strand	75	1	55
β-strand	76-78	3	56
β-strand	79-81	3	54
α-helix	83-88	6
β-strand	90	1	57
β-strand	99-101	3	56
β-strand	108-113	6	52
β-strand	120	1	50
β-strand	130-135	6	54
β-strand	140	1	55
α-helix	142-144	3
β-strand	149	1	57
α-helix	151-155	5
β-strand	159-164	6	54

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Attachment glycoprotein	A, C, E, G	protein	441	Hendra henipavirus	O89343 (AlphaFold model)
Ephrin-B2	B, D, F, H	protein	141	Homo sapiens	P52799 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>6PDL_1 Attachment glycoprotein (chains A, C, E, G)
YRPISQGVSDLVGLPNQICLQKTTSTILKPRLISYTLPINTREGVCITDPLLAVDNGFFA
YSHLEKIGSCTRGIAKQRIIGVGEVLDRGDKVPSMFMTNVWTPPNPSTIHHCSSTYHEDF
YYTLCAVSHVGDPILNSTSWTESLSLIRLAVRPKSDSGDYNQKYIAITKVERGKYDKVMP
YGPSGIKQGDTLYFPAVGFLPRTEFQYNDSNCPIIHCKYSKAENCRLSMGVNSKSHYILR
SGLLKYNLSLGGDIILQFIEIADNRLTIGSPSKIYNSLGQPVFYQASYSWDTMIKLGDVD
TVDPLRVQWRNNSVISRPGQSQCPRFNVCPEVCWEGTYNDAFLIDRLNWVSAGVYLNSNQ
TAENPVFAVFKDNEILYQVPLAEDDTNAQKTITDCFLLENVIWCISLVEIYDTGDSVIRP
KLFAVKIPAQCSESGRGLVPR

Sequence of entity 2 (B, D, F, H), FASTA

>6PDL_2 Ephrin-B2 (chains B, D, F, H)
SIVLEPIYWNSSNSKFLPGQGLVLYPQIGDKLDIICPKVDSKTVGQYEYYKVYMVDKDQA
DRCTIKKENTPLLNCAKPDQDIKFTIKFQEFSPNLWGLEFQKNKDYYIISTSNGSLEGLD
NQEGGVCQTRAMKILMKVGQD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	13

Primary citation

New insights into the Hendra virus attachment and entry process from structures of the virus G glycoprotein and its complex with Ephrin-B2. Xu, K., Chan, Y.P., Rajashankar, K.R. et al. PLoS One (2012) 7:e48742. DOI 10.1371/journal.pone.0048742 · PubMed

Other PDB entries of the same protein (UniProt O89343 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6VY4 2.0 Å, Crystal structure of Hendra receptor binding protein head domain in complex with human…
6PD4 2.2 Å, Crystal Structure of Hendra Virus Attachment G Glycoprotein
6VY6 2.6 Å, Crystal structure of Hendra receptor binding protein head domain in complex with human…
6CMG 2.7 Å, Crystal Structure of the Hendra Virus Attachment G Glycoprotein Bound to a Potent…
6CMI 2.72 Å, Crystal Structure of the Hendra Virus Attachment G Glycoprotein Bound to a Potent…
7SYY 2.74 Å, Hendra virus G protein head domain in complex with cross-neutralizing murine antibody…
7SYZ 2.86 Å, Hendra virus G protein head domain in complex with cross-neutralizing murine antibody…
2X9M 2.9 Å, Hendra virus attachment glycoprotein
8VF1 3.0 Å, Crystal Structure of the Hendra Virus Attachment G glycoprotein (HeV-G)
8JR3 3.22 Å, Crystal structure of Hendra Virus attachment(G) glycoprotein mutant S586N in complex…
2VSK 3.3 Å, Hendra virus attachment glycoprotein in complex with human cell surface receptor ephrinB2
8JR5 3.3 Å, Crystal structure of Hendra Virus attachment(G) glycoprotein mutant S586N

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