8VSE: Human CD45 extracellular region

Cryo-EM structure of human CD45 extracellular region in complex with adenoviral protein E3/49K. Determined by electron microscopy at 3.8 Å resolution. Released 6 Nov 2024.

Method: Electron microscopy
Resolution: 3.8 Å
Organisms: Homo sapiens, Human adenovirus 19a
Chains: 3
Atoms: 8,043
Mol. weight: 165.08 kDa
Ligands: NAG
Released: 6 Nov 2024

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

Secondary structure: helices and β-sheets

8VSE contains 18 α-helices and 93 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: 8 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	225	1	1
α-helix	226-229	4
β-strand	235-240	6	2
β-strand	245-250	6	2
β-strand	257	1	3
β-strand	267-271	5	2
β-strand	277-281	5	4
β-strand	282	1	3
β-strand	287	1	1
α-helix	289-290	2
β-strand	291-295	5	4
β-strand	304-308	5	5
α-helix	312-314	3
β-strand	319-325	7	5
α-helix	333-335	3
β-strand	336-342	7	6
β-strand	345-347	3	6
β-strand	352-354	3	5
β-strand	362-371	10	6
β-strand	375-384	10	6
α-helix	385-387	3
β-strand	394-399	6	7
β-strand	406-411	6	7
β-strand	417	1	8
β-strand	421-425	5	9
β-strand	430-434	5	9
β-strand	441-444	4	7
β-strand	452-458	7	9
β-strand	461-462	2	10
β-strand	466-467	2	10
β-strand	472-477	6	9
α-helix	478-480	3
β-strand	487-493	7	11
β-strand	499-504	6	11
α-helix	505-506	2
β-strand	516-521	6	12
β-strand	526-532	7	12
β-strand	536-539	4	11
β-strand	547-554	8	12
β-strand	555	1	13
β-strand	560	1	13
α-helix	561-563	3
β-strand	564-569	6	12

Chain B: 5 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	225	1	14
α-helix	226-229	4
β-strand	235-240	6	15
β-strand	245-250	6	15
β-strand	267-271	5	15
β-strand	276-281	6	16
β-strand	287	1	14
α-helix	290	1
β-strand	291-296	6	16
β-strand	304-308	5	17
β-strand	319-325	7	17
β-strand	336-342	7	18
β-strand	345-348	4	18
β-strand	351-354	4	17
β-strand	362-371	10	18
β-strand	375-384	10	18
α-helix	385-387	3
β-strand	394-399	6	19
β-strand	406-411	6	19
β-strand	419-425	7	20
β-strand	430-436	7	20
β-strand	441-444	4	19
β-strand	452-462	11	20
β-strand	466-468	3	20
β-strand	472-477	6	20
β-strand	487	1	21
β-strand	491-493	3	22
β-strand	499-502	4	22
β-strand	504	1	21
α-helix	505-506	2
β-strand	515-521	7	23
β-strand	526-532	7	23
β-strand	536-539	4	22
β-strand	547-555	9	23
β-strand	560	1	23
α-helix	562-563	2
β-strand	564-569	6	23

Chain C: 5 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	24
β-strand	13-15	3	25
β-strand	24-27	4	24
β-strand	34-35	2	24
β-strand	38-39	2	24
β-strand	46-48	3	25
β-strand	53-55	3	25
α-helix	60-62	3
β-strand	64-69	6	24
β-strand	76-81	6	24
α-helix	84-88	5
β-strand	89	1	8
α-helix	90-97	8
β-strand	98-103	6	26
β-strand	108-111	4	27
β-strand	119-122	4	26
β-strand	127-130	4	26
β-strand	133-134	2	26
α-helix	137-139	3
β-strand	141-143	3	27
β-strand	147-150	4	27
β-strand	159-164	6	26
β-strand	171-179	9	26
β-strand	247-251	5	28
β-strand	257-260	4	29
β-strand	268-272	5	28
β-strand	288-289	2	29
β-strand	293-296	4	29
α-helix	301-303	3
β-strand	305-311	7	28
β-strand	316-323	8	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Receptor-type tyrosine-protein phosphatase C	A, B	protein	551	Homo sapiens	P08575 (AlphaFold model)
45.5kDa protein	C	protein	343	Human adenovirus 19a	Q67812

Sequence of entity 1 (A, B), FASTA

>8VSE_1 Receptor-type tyrosine-protein phosphatase C (chains A, B)
QSPTPSPTGLTTAKMPSVPLSSDPLPTHTTAFSPASTFERENDFSETTTSLSPDNTSTQV
SPDSLDNASAFNTTGVSSVQTPHLPTHADSQTPSAGTDTQTFSGSAANAKLNPTPGSNAI
SDVPGERSTASTFPTDPVSPLTTTLSLAHHSSAALPARTSNTTITANTSDAYLNASETTT
LSPSGSAVISTTTIATTPSKPTCDEKYANITVDYLYNKETKLFTAKLNVNENVECGNNTC
TNNEVHNLTECKNASVSISHNSCTAPDKTLILDVPPGVEKFQLHDCTQVEKADTTICLKW
KNIETFTCDTQNITYRFQCGNMIFDNKEIKLENLEPEHEYKCDSEILYNNHKFTNASKII
KTDFGSPGEPQIIFCRSEAAHQGVITWNPPQRSFHNFTLCYIKETEKDCLNLDKNLIKYD
LQNLKPYTKYVLSLHAYIIAKVQRNGSAAMCHFTTKSAPPSQVWNMTVSMTSDNSMHVKC
RPPRDRNGPHERYHLEVEAGNTLVRNESHKNCDFRVKDLQYSTDYTFKAYFHNGDYPGEP
FILHHSTSYNS

Sequence of entity 2 (C), FASTA

>8VSE_2 45.5kDa protein (chains C)
GFHTINATWWANITLVGPPDTPVTWYDTQGLWFCNGSRVKNPQIRHTCNDQNLTLIHVNK
TYERTYMGYNRQGTKKEDYKVVVIPPPPATVKPQPEPEYVFVYMGENKTLEGPPGTPVTW
FNQDGKKFCEGEKVLHPEFNHTCDKQNLILLFVNFTHDGAYLGYNHQGTQRTHYEVTVLD
LFPDSGQMKIENHSEETEQKNDEHHNWQKQGGQKQGGQKTNQTKVNDRRKTAQKRPSKLK
PATIEAMLVTVTAGSNLTLVGPKAEGKVTWFDGDLKRPCEPNYRLRHECNNQNLTLINVT
KDYEGTYYGTNDKDEGKRYRVKVNTTNSQSVKIQGAPHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

Primary citation

Orientation-dependent CD45 inhibition with viral and engineered ligands. Borowska, M.T., Liu, L.D., Caveney, N.A. et al. Sci Immunol (2024) 9:eadp0707-eadp0707. DOI 10.1126/sciimmunol.adp0707 · PubMed

Other PDB entries of the same protein (UniProt P08575 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5FN7 2.3 Å, Crystal structure of human CD45 extracellular region, domains d1-d2
1YGR 2.9 Å, Crystal structure of the tandem phosphatase domain of RPTP CD45
1YGU 2.9 Å, Crystal structure of the tandem phosphatase domains of RPTP CD45 with a pTyr peptide
5FMV 2.9 Å, Crystal structure of human CD45 extracellular region, domains d1-d4
5FN6 3.3 Å, Crystal structure of human CD45 extracellular region, domains d1-d3

Browse structure collections

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