21EI: 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: 7
Atoms: 11,865
Mol. weight: 317.76 kDa
Released: 30 Sept 2026

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

Secondary structure: helices and β-sheets

21EI contains 19 α-helices and 140 β-strands across 7 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, 41 β-strands

Element	Residues	Length	Sheet
β-strand	139	1	1
β-strand	144-148	5	2
β-strand	153-156	4	3
β-strand	160	1	1
β-strand	168-170	3	4
β-strand	175-176	2	4
β-strand	184-186	3	3
β-strand	190-194	5	3
α-helix	195-197	3
β-strand	203-204	2	2
β-strand	205-209	5	4
β-strand	214-216	3	4
α-helix	217-219	3
β-strand	220-224	5	2
β-strand	229-232	4	5
β-strand	241	1	6
β-strand	249	1	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	289-296	8	5
β-strand	307-313	7	7
β-strand	319	1	7
β-strand	322-324	3	7
β-strand	326	1	6
β-strand	333-335	3	8
β-strand	342	1	9
α-helix	343-344	2
β-strand	350-355	6	10
β-strand	358-360	3	8
α-helix	363-364	2
β-strand	365-370	6	9
β-strand	373-374	2	9
β-strand	383-388	6	10
β-strand	396-403	8	9
β-strand	408-415	8	9
β-strand	424	1	11
β-strand	434	1	12
β-strand	441-447	7	11
β-strand	456-459	4	13
β-strand	504-511	8	11
β-strand	514-523	10	11
β-strand	530-538	9	13
β-strand	541-549	9	13
β-strand	550	1	12

Chain B: 5 helices, 46 β-strands

Element	Residues	Length	Sheet
β-strand	31-32	2	14
β-strand	39-41	3	15
β-strand	47-53	7	14
β-strand	57-60	4	15
β-strand	81-84	4	14
β-strand	92-98	7	14
β-strand	107-113	7	15
β-strand	121	1	15
β-strand	125-132	8	15
β-strand	139	1	16
β-strand	144-148	5	17
β-strand	153-156	4	18
β-strand	160	1	16
β-strand	167-170	4	19
β-strand	175-176	2	19
β-strand	183-186	4	18
β-strand	190-194	5	18
α-helix	195-198	4
β-strand	203-204	2	17
β-strand	205-209	5	19
β-strand	214-216	3	19
α-helix	217-219	3
β-strand	220-224	5	17
β-strand	229-234	6	20
β-strand	249-256	8	20
β-strand	263-267	5	21
β-strand	277-284	8	20
β-strand	289-296	8	20
β-strand	307-313	7	21
β-strand	318-324	7	21
β-strand	333-337	5	22
β-strand	342-345	4	23
β-strand	352-355	4	24
β-strand	356-360	5	22
α-helix	363-364	2
β-strand	365-370	6	23
β-strand	373-374	2	23
β-strand	383-386	4	24
α-helix	391-393	3
β-strand	395-403	9	23
β-strand	408-418	11	23
β-strand	441-446	6	25
β-strand	457-462	6	26
β-strand	490-491	2	26
α-helix	492	1
β-strand	501-507	7	25
β-strand	510-511	2	27
β-strand	514-515	2	27
β-strand	518-523	6	25
β-strand	530-538	9	26
β-strand	541-549	9	26

Chain C: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	119-128	10
β-strand	132-139	8	38
α-helix	140-143	4
β-strand	150-153	4	39
β-strand	156-163	8	38
β-strand	171-189	19	39
β-strand	197-213	17	39

Chain D: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	117-127	11
β-strand	132-139	8	36
α-helix	140-144	5
β-strand	150-153	4	37
β-strand	156-163	8	36
β-strand	171-189	19	37
β-strand	197-213	17	37

Chain E: 2 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	31-32	2	28
β-strand	38-42	5	29
β-strand	47-53	7	28
β-strand	57-60	4	29
β-strand	81-84	4	28
β-strand	92-98	7	28
β-strand	107-113	7	29
β-strand	121	1	29
β-strand	125-133	9	29
β-strand	139	1	30
β-strand	144-148	5	31
β-strand	153-156	4	32
β-strand	160	1	30
β-strand	168-170	3	33
β-strand	175-176	2	33
β-strand	179	1	32
β-strand	183-186	4	32
β-strand	190-194	5	32
α-helix	195-197	3
β-strand	203-204	2	31
β-strand	205-208	4	33
β-strand	215-216	2	33
α-helix	218-219	2
β-strand	220-224	5	31
β-strand	229-232	4	34
β-strand	250-251	2	34
β-strand	254-256	3	34
β-strand	263-265	3	35
β-strand	278-282	5	34
β-strand	289-295	7	34
β-strand	309-313	5	35
β-strand	318-322	5	35

Chain G: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	119-128	10
β-strand	133-139	7	42
α-helix	140-144	5
β-strand	150-153	4	43
β-strand	156-162	7	42
β-strand	174-175	2	44
β-strand	179-185	7	45
β-strand	186-189	4	43
β-strand	199-205	7	45
β-strand	209-210	2	44

Chain H: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
α-helix	116-127	12
β-strand	134-139	6	40
β-strand	150-152	3	41
β-strand	156-161	6	40
β-strand	171-189	19	41
β-strand	197-213	17	41

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vascular endothelial growth factor receptor 3	A, B, E	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), FASTA

>21EI_1 Vascular endothelial growth factor receptor 3 (chains A, B, E)
MQRGAALCLRLWLCLGLLDGLVSGYSMTPPTLNITEESHVIDTGDSLSISCRGQHPLEWA
WPGAQEAPATGDKDSEDTGVVRDCEGTDARPYCKVLLLHEVHANDTGSYVCYYKYIKARI
EGTTAASSYVFVRDFEQPFINKPDTLLVNRKDAMWVPCLVSIPGLNVTLRSQSSVLWPDG
QEVVWDDRRGMLVSTPLLHDALYLQCETTWGDQDFLSNPFLVHITGNELYDIQLLPRKSL
ELLVGEKLVLNCTVWAEFNSGVTFDWDYPGKQAERGKWVPERRSQQTHTELSSILTIHNV
SQHDLGSYVCKANNGIQRFRESTEVIVHENPFISVEWLKGPILEATAGDELVKLPVKLAA
YPPPEFQWYKDGKALSGRHSPHALVLKEVTEASTGTYTLALWNSAAGLRRNISLELVVNV
PPQIHEKEASSPSIYSRHSRQALTCTAYGVPLPLSIQWHWRPWTPCKMFAQRSLRRRQQQ
DLMPQCRDWRAVTTQDAVNPIESLDTWTEFVEGKNKTVSKLVIQNANVSAMYKCVVSNKV
GQDERLIYFYVTTIPDGFTIESKPSEELLEGQPVLLSCQADSYKYEHLRWYRLNLSTLHD
AHGNPLLLDCKNVHLFATPLAASLEEVAPGARHATLSLSIPRVAPEHEGHYVCEVQDRRS
HDKHCHKKYLSVQALEAPRLTQNLTDLLVNVSDSLEMQCLVAGAHAPSIVWYKDERLLEE
KSGVDLADSNQKLSIQRVREEDAGRYLCSVCNAKGCVNSSASVAVEGSEDLKLEVLFQ

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

>21EI_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
21ES 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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