5DFV: Human CD81 large extracellular loop

Crystal structure of human CD81 large extracellular loop in complex with murine FAB fragment K04. Determined by X-ray diffraction at 2.8 Å resolution. Released 16 Dec 2015.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Homo sapiens, Mus musculus
Chains: 6
Atoms: 7,930
Mol. weight: 117.18 kDa
Released: 16 Dec 2015

Explore 5DFV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5DFV contains 39 α-helices and 90 β-strands across 6 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, 0 β-strands

Element	Residues	Length
α-helix	116-136	21
α-helix	141-154	14
α-helix	163-171	9
α-helix	185-187	3
α-helix	190-198	9

Chain B: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	116-136	21
α-helix	141-154	14
α-helix	160-162	3
α-helix	163-171	9
α-helix	183-188	6
α-helix	190-199	10

Chain C: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	103-106	4	1
β-strand	110-112	3	2
β-strand	118-125	8	1
α-helix	154-156	3
β-strand	197-204	7	2
β-strand	211-253	7	2
β-strand	291-293	3	2
β-strand	298	1	1
β-strand	302-307	6	1
β-strand	312-317	6	1
α-helix	322-324	3
β-strand	326-332	7	2
β-strand	399-401	2	2
β-strand	405-409	5	2
α-helix	1000-1002	3
β-strand	1003	1	3
β-strand	1006-1010	5	4
β-strand	1023-1031	9	4
β-strand	1032	1	3
β-strand	1037-1040	4	5
α-helix	1041-1043	3
β-strand	1045	1	5
β-strand	1049-1051	3	4
α-helix	1052-1054	3
β-strand	1055-1056	2	4
β-strand	1061-1068	8	4
β-strand	1080-1085	6	5
α-helix	1086-1088	3
β-strand	1090-1095	6	5

Chain D: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	504-507	4	6
β-strand	510-513	4	7
β-strand	519-552	7	6
β-strand	598-604	6	7
α-helix	609-610	2
β-strand	611-615	5	7
β-strand	696-697	2	7
α-helix	698	1
β-strand	706-711	6	6
β-strand	716-721	6	6
α-helix	726-728	3
β-strand	731-752	6	7
α-helix	798	1
β-strand	801	1	7
β-strand	805-809	5	7
β-strand	2003	1	8
β-strand	2006-2010	5	9
α-helix	2011-2013	3
α-helix	2014-2018	5
β-strand	2022-2031	10	9
β-strand	2032	1	8
β-strand	2037-2042	6	10
β-strand	2046	1	10
β-strand	2051-2053	3	9
α-helix	2055-2059	5
β-strand	2065-2073	9	9
α-helix	2075-2078	4
β-strand	2084-2089	6	10
β-strand	2097	1	10
β-strand	2100-2101	2	10

Chain E: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	103-106	4	11
α-helix	107	1
β-strand	110-112	3	12
β-strand	118-125	8	11
α-helix	154-156	3
β-strand	197-204	7	12
β-strand	211-253	7	12
β-strand	290-293	4	12
α-helix	295-297	3
β-strand	302-307	6	11
β-strand	312-317	6	11
α-helix	322-324	3
β-strand	326-332	7	12
β-strand	399-401	2	12
β-strand	405-409	5	12
β-strand	1003	1	13
α-helix	1004-1005	2
β-strand	1006-1010	5	14
β-strand	1022-1031	10	14
β-strand	1032	1	13
β-strand	1037-1040	4	15
β-strand	1045	1	15
β-strand	1049-1051	3	14
α-helix	1052-1054	3
β-strand	1055-1057	3	14
β-strand	1060-1069	10	14
β-strand	1080-1085	6	15
α-helix	1086-1088	3
β-strand	1090-1095	6	15

Chain F: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	504-507	4	16
β-strand	510-514	5	17
β-strand	519-552	7	16
β-strand	563	1	18
β-strand	596	1	18
β-strand	598-604	6	17
β-strand	611-615	5	17
β-strand	696-697	2	17
α-helix	698	1
β-strand	706-711	6	16
β-strand	716-721	6	16
α-helix	726-728	3
β-strand	730-752	7	17
α-helix	798	1
β-strand	799-801	2	17
β-strand	805-810	6	17
β-strand	2003	1	19
β-strand	2008-2010	3	20
α-helix	2011-2013	3
α-helix	2014-2018	5
β-strand	2021-2031	11	20
β-strand	2032	1	19
β-strand	2036-2042	7	21
β-strand	2045-2046	2	21
β-strand	2051-2055	5	20
α-helix	2056-2059	4
β-strand	2065-2074	10	20
α-helix	2075-2080	6
β-strand	2083-2090	8	21
β-strand	2097-2102	6	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CD81 antigen	A, B	protein	99	Homo sapiens	P60033 (AlphaFold model)
FAB heavy chain	C, E	protein	222	Mus musculus
FAB light chain	D, F	protein	218	Mus musculus

Sequence of entity 1 (A, B), FASTA

>5DFV_1 CD81 antigen (chains A, B)
GSGFVNKDQIAKDVKQFYDQALQQAVVDDDANNAKAVVKTFHETLDCCGSSTLTALTTSV
LKNNLCPSGSNIISNLFKEDCHQKIDDLFSGKHHHHHHH

Sequence of entity 2 (C, E), FASTA

>5DFV_2 FAB HEAVY CHAIN (chains C, E)
QVQLQQSGPELVKPGASVKISCKASGYTFSSSWMNWVKQRPGKGLEWIGRIYSGDGDAIY
NGKFKGKATLTADKSSSTAYMQLSSLTSEDSAVYFCAREGKTGDLLLRSWGQGSALTVSS
AKTTAPSVYPLVPVCGGTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPALLQSG
LYTLSSSVTVTSNTWPSQTITCNVAHPASSTKVDKKIEPRVP

Sequence of entity 3 (D, F), FASTA

>5DFV_3 FAB LIGHT CHAIN (chains D, F)
DIVLTQSPASLSVSLGQRATISCRASKSVSTSIYSYMHWYQQKPGQPPKLLIKYASYLES
GVPARFSGSGSGTDFTLNIHPVEEEDAATYYCEHSREFPFTFGTGTKLEIKRADAAPTVS
IFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMS
STLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Primary citation

VH-VL orientation prediction for antibody humanization candidate selection: A case study. Bujotzek, A., Lipsmeier, F., Harris, S.F. et al. MAbs (2016) 8:288-305. DOI 10.1080/19420862.2015.1117720 · PubMed

Other PDB entries of the same protein (UniProt P60033 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5M33 1.28 Å, Structural tuning of CD81LEL (space group P21)
1G8Q 1.6 Å, Crystal structure of human CD81 extracellular domain, A receptor for hepatitis C virus
3X0E 1.84 Å, Crystal structure of the ectodomain of human CD81 large extracellular loop (hCD81-LEL)
5M2C 1.96 Å, Structural tuning of CD81LEL (space group P32 1 2)
5M3T 2.02 Å, Structural tuning of CD81LEL (space group P64)
6EJM 2.15 Å, Crystal structure of human CD81 large extracellular loop in complex with single chain fv…
5DFW 2.33 Å, Crystal structure of human CD81 large extracellular loop in complex with single chain fv…
5M3D 2.38 Å, Structural tuning of CD81LEL (space group P31)
6U9S 2.4 Å, Crystal structure of human CD81 large extracellular loop in complex with 5A6 Fab
1IV5 2.6 Å, New Crystal Form of Human CD81 Large Extracellular Loop.
6EK2 2.65 Å, Crystal structure of human CD81 large extracellular loop in complex with single chain fv…
6EJG 2.82 Å, Crystal structure of human CD81 large extracellular loop in complex with single chain fv…

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