7A3N: Zika virus envelope glycoprotein

Crystal structure of Zika virus envelope glycoprotein in complex with the Fab fragment of the broadly neutralizing human antibody EDE1 C10. Determined by X-ray diffraction at 2.1 Å resolution. Released 8 Dec 2021.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Zika virus, Homo sapiens
Chains: 3
Atoms: 6,542
Mol. weight: 96.97 kDa
Ligands: CA
Released: 8 Dec 2021

Explore 7A3N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7A3N contains 26 α-helices and 82 β-strands across 3 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: 14 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	1
α-helix	14-15	2
β-strand	20-26	7	2
β-strand	30-34	5	1
β-strand	41-50	10	1
β-strand	54-72	19	1
α-helix	83-86	4
β-strand	90-99	10	1
α-helix	101-103	3
β-strand	109-129	21	1
α-helix	132-134	3
β-strand	135-143	9	1
α-helix	147-148	2
β-strand	164-169	6	1
β-strand	170	1	3
β-strand	173	1	3
β-strand	175-179	5	2
α-helix	181-183	3
β-strand	184	1	4
β-strand	185-190	6	2
β-strand	201-206	6	1
β-strand	209-214	6	1
α-helix	215-219	5
β-strand	225-227	3	1
β-strand	237	1	1
α-helix	239-242	4
β-strand	243-248	6	5
β-strand	252-257	6	5
α-helix	262-268	7
β-strand	273-278	6	1
β-strand	281-284	4	1
β-strand	288-294	7	2
β-strand	298	1	4
α-helix	305	1
β-strand	306-307	2	6
α-helix	308	1
β-strand	312-314	3	7
β-strand	319-320	2	7
β-strand	326-332	7	7
β-strand	339-340	2	6
α-helix	341-342	2
β-strand	343-346	4	8
β-strand	355	1	8
β-strand	357-358	2	7
β-strand	364-365	2	6
β-strand	372-379	8	7
α-helix	380-381	2
β-strand	383-389	7	8
α-helix	392-394	3
β-strand	396-402	7	8

Chain H: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	9
α-helix	7-9	3
β-strand	10-12	3	10
β-strand	18-25	8	9
α-helix	29-31	3
β-strand	32-39	8	10
β-strand	45-52	8	10
β-strand	57-59	3	10
α-helix	61-63	3
β-strand	67-72	6	9
β-strand	77-82	6	9
α-helix	84-86	3
β-strand	88-96	9	10
β-strand	103	1	10
β-strand	107-111	5	10
β-strand	117	1	11
β-strand	120-124	5	12
β-strand	136-145	10	12
β-strand	146	1	11
β-strand	151-154	4	13
α-helix	155-157	3
β-strand	163-165	3	12
α-helix	166-168	3
β-strand	169-170	2	12
β-strand	176-184	9	12
α-helix	186-188	3
β-strand	194-200	7	13
β-strand	205-211	7	13

Chain L: 5 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	14
β-strand	5	1	15
β-strand	9-13	4	16
β-strand	19-24	6	15
β-strand	33-38	6	16
β-strand	45-48	4	16
β-strand	49	1	17
β-strand	53	1	17
β-strand	62-67	6	15
β-strand	70-75	6	15
α-helix	80-82	3
β-strand	84-91	8	16
β-strand	96-98	3	16
β-strand	99	1	14
β-strand	102-106	5	16
β-strand	111	1	18
α-helix	112-113	2
β-strand	114-118	5	19
α-helix	122-126	5
β-strand	130-139	10	19
β-strand	140	1	18
β-strand	145-150	6	20
β-strand	154-155	2	20
β-strand	159-161	3	19
α-helix	162-164	3
β-strand	165-166	2	19
β-strand	172-180	9	19
α-helix	182-187	6
β-strand	191-197	7	20
β-strand	200-205	6	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Core protein	A	protein	414	Zika virus	A0A024B7W1 (AlphaFold model)
EDE1 C10 Fab	H	protein	268	Homo sapiens
EDE1 C10 Fab	L	protein	217	Homo sapiens

Sequence of entity 1 (A), FASTA

>7A3N_1 Core protein (chains A)
IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYC
YEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFA
CSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATL
GGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKE
ALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRL
KGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLIT
ANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTIGKGLVPR

Sequence of entity 2 (H), FASTA

>7A3N_2 EDE1 C10 Fab (chains H)
EVQLVESGAEVKKPGASVKVSCKASGYTFTSYAMHWVRQAPGQRLEWMGWINAGNGNTKY
SQKFQDRVTITRDTSASTAYMELSSLRSEDTAIYYCARDKVDDYGDYWFPTLWYFDYWGQ
GTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCLEDDDDKAG
WSHPQFEKGGGSGGGSGGGSWSHPQFEK

Sequence of entity 3 (L), FASTA

>7A3N_3 EDE1 C10 Fab (chains L)
SQSALTQPASVSGSPGQSITISCTGTSSDVGGFNYVSWFQQHPGKAPKLMLYDVTSRPSG
VSSRFSGSKSGNTASLTISGLQAEDEADYYCSSHTSRGTWVFGGGTKLTVLGQPKAAPSV
TLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAAS
SYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

Primary citation

The epitope arrangement on flavivirus particles contributes to Mab C10's extraordinary neutralization breadth across Zika and dengue viruses. Sharma, A., Zhang, X., Dejnirattisai, W. et al. Cell (2021) 184:6052-6066.e18. DOI 10.1016/j.cell.2021.11.010 · PubMed

Other PDB entries of the same protein (UniProt A0A024B7W1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5KQR 1.33 Å, Structure of NS5 methyltransferase from Zika virus bound to S-adenosylmethionine
6LD1 1.4 Å, Zika NS5 polymerase domain
6LD2 1.4 Å, Zika NS5 polymerase domain
5KQS 1.5 Å, Structure of NS5 methyltransferase from Zika virus bound to S-adenosylmethionine and…
6LD4 1.5 Å, Zika NS5 polymerase domain
6S0J 1.5 Å, Structure of Zika virus NS3 helicase in complex with ADP-MgF3(H2O)-
5ULP 1.55 Å, Structure of the NS5 methyltransferase from Zika bound to MS2042
5Y6N 1.57 Å, Zika virus helicase in complex with ADP
7M1V 1.6 Å, Structure of Zika virus NS2b-NS3 protease mutant binding the compound NSC86314 in the…
5KVE 1.7 Å, Zika specific antibody, ZV-48, bound to ZIKA envelope DIII
6RWZ 1.7 Å, Structure of Zika virus NS3 helicase in complex with ADP-BeF3
5JMT 1.8 Å, Crystal structure of Zika virus NS3 helicase

Browse structure collections

About this viewer

MolViewer shows 7A3N directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.