21ES: Vascular endothelial growth factor receptor 3

Structural and Functional Insights into VEGFR-3-Mediated Lymphangiogenesis : Unraveling the clustering mechanism of VEGFR-3/VEGF-C. Determined by electron microscopy at 3.3 Å resolution. Released 30 Sept 2026.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 8
Atoms: 15,431
Mol. weight: 405.26 kDa
Released: 30 Sept 2026

Explore 21ES in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

21ES contains 25 α-helices and 195 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: 5 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	139	1	1
β-strand	145-148	4	2
β-strand	153-156	4	3
β-strand	160	1	1
β-strand	167-170	4	4
β-strand	175-176	2	4
β-strand	184-186	3	3
β-strand	190-194	5	3
β-strand	203-204	2	2
β-strand	205-208	4	4
β-strand	215-216	2	4
α-helix	218-219	2
β-strand	220-224	5	2
β-strand	229-232	4	5
β-strand	241	1	6
β-strand	248-251	4	5
β-strand	254-256	3	5
β-strand	263-267	5	7
α-helix	269-271	3
β-strand	277-284	8	5
β-strand	289-297	9	5
β-strand	307-313	7	7
β-strand	318-324	7	7
β-strand	326	1	6
β-strand	332-337	6	8
β-strand	346	1	9
β-strand	347	1	10
β-strand	349	1	10
β-strand	350-355	6	11
β-strand	356-361	6	8
β-strand	365-370	6	12
β-strand	373-374	2	12
β-strand	383-388	6	11
α-helix	391-393	3
β-strand	395-403	9	12
β-strand	408-416	9	12
β-strand	419	1	9
α-helix	420-422	3
β-strand	441	1	13
β-strand	444-445	2	14
α-helix	452-453	2
β-strand	457-462	6	15
β-strand	504-511	8	14
β-strand	514-521	8	14
β-strand	523	1	13
β-strand	530-538	9	15
β-strand	541-549	9	15

Chain B: 5 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	145-148	4	16
β-strand	153-156	4	17
β-strand	168-171	4	16
β-strand	175-176	2	16
β-strand	183-186	4	17
β-strand	190-194	5	17
α-helix	195-198	4
β-strand	203-207	5	16
β-strand	208-209	2	18
β-strand	214-215	2	18
β-strand	220-224	5	16
β-strand	232	1	19
β-strand	254-256	3	19
β-strand	263-267	5	20
β-strand	277-279	3	21
β-strand	282-284	3	19
β-strand	289-291	3	19
β-strand	294-296	3	21
β-strand	308-313	6	20
β-strand	318-323	6	20
β-strand	333-336	4	22
β-strand	342-346	5	23
β-strand	352-355	4	24
β-strand	357-360	4	22
β-strand	365-370	6	23
β-strand	373-374	2	23
α-helix	375-376	2
β-strand	383-386	4	24
β-strand	395-403	9	23
β-strand	408-419	12	23
α-helix	425-427	3
α-helix	430-432	3
β-strand	441-447	7	25
β-strand	456-462	7	26
β-strand	490-491	2	26
α-helix	500	1
β-strand	501-511	11	25
β-strand	514-523	10	25
β-strand	530-538	9	26
β-strand	541-549	9	26

Chain C: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
α-helix	116-127	12
β-strand	134-139	6	60
β-strand	150-151	2	61
β-strand	156-161	6	60
β-strand	171-175	5	62
β-strand	178-187	10	63
β-strand	188-189	2	61
β-strand	197-206	10	63
β-strand	209-213	5	62

Chain D: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	117-127	11
β-strand	132-139	8	64
α-helix	140	1
α-helix	141-145	5
β-strand	156-163	8	64
β-strand	172-175	4	65
β-strand	178-185	8	66
β-strand	199-206	8	66
β-strand	209-212	4	65

Chain E: 4 helices, 49 β-strands

Element	Residues	Length	Sheet
β-strand	139	1	27
α-helix	141-143	3
β-strand	144-148	5	28
β-strand	153-156	4	29
β-strand	160	1	27
β-strand	167-170	4	30
β-strand	175-176	2	30
β-strand	184-186	3	29
β-strand	190-194	5	29
α-helix	195-197	3
β-strand	203-204	2	28
β-strand	205-208	4	30
β-strand	216	1	30
α-helix	217-219	3
β-strand	220-224	5	28
β-strand	229-232	4	31
β-strand	249-250	2	32
β-strand	254-256	3	31
β-strand	263-267	5	33
β-strand	277-278	2	32
β-strand	281-282	2	31
β-strand	289-292	4	31
β-strand	295-296	2	32
β-strand	308-313	6	33
β-strand	318-323	6	33
β-strand	337	1	34
β-strand	346	1	35
β-strand	355	1	36
β-strand	356	1	34
β-strand	367-368	2	37
β-strand	369-370	2	38
β-strand	373-374	2	38
β-strand	383	1	36
β-strand	399-400	2	37
β-strand	401-403	3	39
β-strand	408-410	3	39
β-strand	419	1	35
β-strand	435-436	2	40
β-strand	441-443	3	41
β-strand	446-447	2	41
α-helix	452-453	2
β-strand	459-460	2	42
β-strand	490-491	2	42
β-strand	501-508	8	41
β-strand	511	1	43
β-strand	514	1	43
β-strand	517-523	7	41
β-strand	530-532	3	44
β-strand	533	1	42
β-strand	536-537	2	45
β-strand	542-543	2	45
β-strand	547-549	3	44
β-strand	551-552	2	40

Chain F: 3 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	139	1	46
β-strand	145-147	3	47
β-strand	153-156	4	48
β-strand	160	1	46
β-strand	167-170	4	49
β-strand	175	1	49
β-strand	183-186	4	48
β-strand	190-194	5	48
β-strand	203-204	2	47
β-strand	205-208	4	49
β-strand	209	1	50
β-strand	214	1	50
β-strand	220-223	4	47
β-strand	231-232	2	51
β-strand	240-241	2	52
β-strand	248-251	4	51
β-strand	254-256	3	51
β-strand	264	1	53
β-strand	267	1	53
α-helix	269-271	3
β-strand	277-284	8	51
β-strand	289-297	9	51
β-strand	307-313	7	53
β-strand	318-324	7	53
β-strand	325-326	2	52
β-strand	344-346	3	54
β-strand	352-355	4	55
β-strand	366-370	5	56
β-strand	373-374	2	56
β-strand	383-386	4	55
α-helix	391-393	3
β-strand	395-403	9	56
β-strand	408-416	9	56
β-strand	417-419	3	54
β-strand	435	1	57
β-strand	445-447	3	58
α-helix	452-453	2
β-strand	456-459	4	59
β-strand	504-511	8	58
β-strand	514-521	8	58
β-strand	530-537	8	59
β-strand	542-543	2	59
β-strand	546-549	4	59
β-strand	551	1	57

Chain G: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	117-127	11
β-strand	132-139	8	67
α-helix	140-143	4
β-strand	150-153	4	68
β-strand	156-163	8	67
β-strand	171-189	19	68
β-strand	192	1	69
β-strand	194	1	69
β-strand	197-213	17	68

Chain H: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	117-127	11
β-strand	132-139	8	70
α-helix	140-144	5
β-strand	151-153	3	71
β-strand	156-163	8	70
β-strand	171-175	5	72
β-strand	178-188	11	71
β-strand	197-206	10	71
β-strand	209-213	5	72

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vascular endothelial growth factor receptor 3	A, B, E, F	protein	778	Homo sapiens	P35916 (AlphaFold model)
Vascular endothelial growth factor C	C, D, G, H	protein	125	Homo sapiens	P49767 (AlphaFold model)

Sequence of entity 1 (A, B, E, F), FASTA

>21ES_1 Vascular endothelial growth factor receptor 3 (chains A, B, E, F)
MQRGAALCLRLWLCLGLLDGLVSGYSMTPPTLNITEESHVIDTGDSLSISCRGQHPLEWA
WPGAQEAPATGDKDSEDTGVVRDCEGTDARPYCKVLLLHEVHANDTGSYVCYYKYIKARI
EGTTAASSYVFVRDFEQPFINKPDTLLVNRKDAMWVPCLVSIPGLNVTLRSQSSVLWPDG
QEVVWDDRRGMLVSTPLLHDALYLQCETTWGDQDFLSNPFLVHITGNELYDIQLLPRKSL
ELLVGEKLVLNCTVWAEFNSGVTFDWDYPGKQAERGKWVPERRSQQTHTELSSILTIHNV
SQHDLGSYVCKANNGIQRFRESTEVIVHENPFISVEWLKGPILEATAGDELVKLPVKLAA
YPPPEFQWYKDGKALSGRHSPHALVLKEVTEASTGTYTLALWNSAAGLRRNISLELVVNV
PPQIHEKEASSPSIYSRHSRQALTCTAYGVPLPLSIQWHWRPWTPCKMFAQRSLRRRQQQ
DLMPQCRDWRAVTTQDAVNPIESLDTWTEFVEGKNKTVSKLVIQNANVSAMYKCVVSNKV
GQDERLIYFYVTTIPDGFTIESKPSEELLEGQPVLLSCQADSYKYEHLRWYRLNLSTLHD
AHGNPLLLDCKNVHLFATPLAASLEEVAPGARHATLSLSIPRVAPEHEGHYVCEVQDRRS
HDKHCHKKYLSVQALEAPRLTQNLTDLLVNVSDSLEMQCLVAGAHAPSIVWYKDERLLEE
KSGVDLADSNQKLSIQRVREEDAGRYLCSVCNAKGCVNSSASVAVEGSEDLKLEVLFQ

Sequence of entity 2 (C, D, G, H), FASTA

>21ES_2 Vascular endothelial growth factor C (chains C, D, G, H)
SGGSTEETIKFAAAHYNTEILKSIDNEWRKTQCMPREVAIDVGKEFGVATNTFFKPPCVS
VYRCGGCCNSEGLQCMNTSTSYLSKTLFEITVPLSQGPKPVTISFANHTSCRCMSKLGSH
HHHHH

Primary citation

Structural Basis of Lymphangiogenic Receptor VEGFR-3 Activation Mediated by Distinctive Clustering of the Ligand-Receptor Complex. Cho, R., Ahn, J., Yang, J. et al. Adv Sci (Weinh) (2026):e77728-e77728. DOI 10.1002/advs.77728 · PubMed

Other PDB entries of the same protein (UniProt P35916 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4BSJ 2.5 Å, Crystal structure of VEGFR-3 extracellular domains D4-5
21EI 3.3 Å, Structural and Functional Insights into VEGFR-3-Mediated Lymphangiogenesis : Unraveling…
4BSK 4.2 Å, Crystal structure of VEGF-C in complex with VEGFR-3 domains D1-2

Browse structure collections

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