8K3C: Light chain of 41-6 Fab fragment

Nipah virus Attachment glycoprotein with 41-6 antibody fragment. Determined by electron microscopy at 2.88 Å resolution. Released 1 May 2024.

Method: Electron microscopy
Resolution: 2.88 Å
Organisms: Homo sapiens, Henipavirus nipahense
Chains: 4
Atoms: 10,813
Mol. weight: 154.04 kDa
Released: 1 May 2024

Explore 8K3C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8K3C contains 29 α-helices and 124 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
α-helix	133-145	13
α-helix	159-161	3
β-strand	179	1	18
β-strand	199-202	4	18
α-helix	210-212	3
β-strand	216-224	9	19
β-strand	228-237	10	19
β-strand	244-257	14	19
β-strand	263-271	9	19
β-strand	279-286	8	20
β-strand	290-297	8	20
β-strand	315-320	6	20
α-helix	328-331	4
β-strand	332-336	5	20
β-strand	347-350	4	21
β-strand	354	1	20
β-strand	356-358	3	21
β-strand	361-371	11	21
α-helix	372-374	3
α-helix	379-381	3
α-helix	394-397	4
β-strand	407-417	11	21
β-strand	428-430	3	21
β-strand	431	1	22
α-helix	432	1
β-strand	438	1	21
β-strand	442-447	6	23
β-strand	450-455	6	23
β-strand	465-471	7	23
β-strand	475	1	22
β-strand	476-479	4	23
β-strand	509	1	18
β-strand	512-515	4	24
β-strand	520-526	7	24
β-strand	533	1	18
β-strand	535-540	6	24
β-strand	545-550	6	24
β-strand	557-567	11	18
β-strand	572-581	10	18
β-strand	591	1	18
β-strand	593-596	4	18
α-helix	597-598	2

Chain B: 12 helices, 38 β-strands

Element	Residues	Length	Sheet
α-helix	132-145	14
α-helix	151-153	3
β-strand	178-179	2	25
α-helix	186-189	4
β-strand	201-202	2	25
α-helix	204-206	3
β-strand	215-218	4	26
β-strand	222-225	4	26
β-strand	228-237	10	26
β-strand	244-257	14	26
β-strand	263-271	9	26
β-strand	279-286	8	27
β-strand	290-297	8	27
β-strand	299	1	28
β-strand	301	1	28
α-helix	307-309	3
β-strand	314-320	7	27
α-helix	323-324	2
β-strand	332-336	5	27
β-strand	340-341	2	29
β-strand	347-350	4	29
β-strand	354	1	27
β-strand	356-358	3	29
β-strand	361-371	11	29
α-helix	372-374	3
α-helix	379-381	3
α-helix	394-397	4
β-strand	407-417	11	29
α-helix	418-420	3
β-strand	426-430	5	29
β-strand	431	1	30
α-helix	432	1
β-strand	442-447	6	31
β-strand	450-455	6	31
β-strand	463	1	32
β-strand	465-471	7	31
β-strand	475	1	30
β-strand	476-479	4	31
β-strand	486	1	32
β-strand	509	1	25
β-strand	511-513	3	33
β-strand	521-526	6	33
β-strand	533	1	34
β-strand	535-540	6	33
β-strand	545-550	6	33
β-strand	557	1	34
β-strand	558-568	11	25
β-strand	572-582	11	25
β-strand	587-596	10	25
α-helix	597-598	2

Chain C: 4 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	8
β-strand	10-12	3	9
β-strand	17-25	9	8
β-strand	33-38	6	10
β-strand	41	1	11
β-strand	43	1	11
β-strand	46-51	6	10
β-strand	58-60	3	10
β-strand	68-73	6	8
β-strand	78-84	7	8
α-helix	88-90	3
β-strand	92-94	3	9
β-strand	95-99	5	10
β-strand	101-102	2	12
β-strand	105	1	13
β-strand	112	1	13
β-strand	115-116	2	12
β-strand	121	1	10
β-strand	122	1	8
β-strand	125-129	5	9
α-helix	135-137	3
β-strand	138-142	5	14
α-helix	146-149	4
β-strand	153-156	4	15
β-strand	157-163	7	14
β-strand	169-172	4	16
β-strand	182-183	2	17
α-helix	184-186	3
β-strand	187-188	2	14
β-strand	194-197	4	14
β-strand	198-199	2	17
β-strand	200-203	4	15
β-strand	213-218	6	16
β-strand	223-228	6	16

Chain D: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	1
β-strand	11	1	2
β-strand	17-23	7	1
α-helix	26-30	5
β-strand	34-39	6	3
β-strand	46-49	4	3
β-strand	50	1	4
β-strand	54	1	4
β-strand	63-68	6	1
β-strand	71-77	7	1
α-helix	81-83	3
β-strand	86-93	8	3
β-strand	98-101	4	3
β-strand	105-106	2	3
β-strand	108	1	2
β-strand	115	1	5
β-strand	118-121	4	6
α-helix	126-130	5
β-strand	134-143	10	6
β-strand	144	1	5
β-strand	148-154	7	7
β-strand	157-158	2	7
β-strand	163-165	3	6
β-strand	176-184	9	6
α-helix	186-190	5
β-strand	195-201	7	7
β-strand	204-210	7	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Light chain of 41-6 Fab fragment	D	protein	216	Homo sapiens
Heavy chain of 41-6 Fab fragments	C	protein	238	Homo sapiens
Glycoprotein G	A, B	protein	471	Henipavirus nipahense	Q9IH62 (AlphaFold model)

Sequence of entity 1 (D), FASTA

>8K3C_1 Light chain of 41-6 Fab fragment (chains D)
QSVVTQPPSVSAAPGQKVTISCSGSSSNIGTNHLSWYQQVPGTAPKLLIYDNNKRPSGIP
DRFSGSKSGTSASLAISGLQSEDEADYYCATWDDSLHAWVFGGGTKLTVLGQPKAAPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 2 (C), FASTA

>8K3C_2 Heavy chain of 41-6 Fab fragments (chains C)
EVQLVQSGGGLVQPGGSLRLSCAASGFTVSSNYMSWVRQAPGKGLEWVSAISGSGGSTYY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDREDIVVVPAPRGYYYYYYMDV
WGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSG
VHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTS

Sequence of entity 3 (A, B), FASTA

>8K3C_3 Glycoprotein G (chains A, B)
ISQSTASINENVNEKCKFTLPPLKIHECNISCPNPLPFREYRPQTEGVSNLVGLPNNICL
QKTSNQILKPKLISYTLPVVGQSGTCITDPLLAMDEGYFAYSHLERIGSCSRGVSKQRII
GVGEVLDRGDEVPSLFMTNVWTPPNPNTVYHCSAVYNNEFYYVLCAVSTVGDPILNSTYW
SGSLMMTRLAVKPKSNGGGYNQHQLALRSIEKGRYDKVMPYGPSGIKQGDTLYFPAVGFL
VRTEFKYNDSNCPITKCQYSKPENCRLSMGIRPNSHYILRSGLLKYNLSDGENPKVVFIE
ISDQRLSIGSPSKIYDSLGQPVFYQASFSWDTMIKFGDVLTVNPLVVNWRNNTVISRPGQ
SQCPRFNTCPEICWEGVYNDAFLIDRINWISAGVFLDSNQTAENPVFTVFKDNEILYRAQ
LASEDTNAQKTITNCFLLKNKIWCISLVEIYDTGDNVIRPKLFAVKIPEQC

Primary citation

Potent human neutralizing antibodies against Nipah virus derived from two ancestral antibody heavy chains. Chen, L., Sun, M., Zhang, H. et al. Nat Commun (2024) 15:2987-2987. DOI 10.1038/s41467-024-47213-8 · PubMed

Other PDB entries of the same protein (UniProt Q9IH62 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2VSM 1.8 Å, Nipah virus attachment glycoprotein in complex with human cell surface receptor ephrinB2
2VWD 2.25 Å, Nipah Virus Attachment Glycoprotein
3D11 2.31 Å, Crystal Structures of the Nipah G Attachment Glycoprotein
8JA5 2.79 Å, Crystal structure of Nipah Virus attachment (G) glycoprotein in complex with…
8K0D 2.94 Å, Cryo-EM structure of conformation 2 of complex of Nipah virus attachment G with 1E5…
9LU3 3.0 Å, LN1F9 Fab bound to Nipah Virus attachment (G) glycoprotein head domain
3D12 3.0 Å, Crystal Structures of Nipah Virus G Attachment Glycoprotein in Complex with its Receptor…
9LUE 3.03 Å, Cryo-EM structure of the Nipah G head domain in complex with three Fabs
8K0C 3.18 Å, Cryo-EM structure of conformation 1 of complex of Nipah virus attachment glycoprotein G…
7TXZ 3.2 Å, Nipah Virus attachment (G) glycoprotein ectodomain in complex with nAH1.3 neutralizing…
6VY5 3.4 Å, Crystal structure of Nipah receptor binding protein head domain in complex with human…
7TY0 3.5 Å, Nipah Virus attachment (G) glycoprotein ectodomain in complex with nAH1.3 neutralizing…

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