6EJG: Human CD81 large extracellular loop

Crystal structure of human CD81 large extracellular loop in complex with single chain fv fragment 4. Determined by X-ray diffraction at 2.82 Å resolution. Released 30 May 2018.

Method: X-ray diffraction
Resolution: 2.82 Å
Organisms: Homo sapiens, Mus musculus
Chains: 4
Atoms: 4,971
Mol. weight: 74.64 kDa
Released: 30 May 2018

Explore 6EJG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6EJG contains 23 α-helices and 48 β-strands across 4 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: 7 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	176	1
α-helix	182-187	6
α-helix	190-198	9

Chain B: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	116-135	20
α-helix	141-153	13
α-helix	163-171	9
α-helix	182-187	6
α-helix	190-199	10

Chain C: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	42-45	4	1
β-strand	48-51	4	2
β-strand	57-63	7	1
β-strand	75-80	6	2
α-helix	85-86	2
β-strand	87-91	5	2
β-strand	95-96	2	2
α-helix	97	1
β-strand	104-109	6	1
β-strand	112-117	6	1
α-helix	122-124	3
β-strand	127-132	6	2
α-helix	138	1
β-strand	140	1	2
β-strand	144-148	5	2
β-strand	172-175	4	3
β-strand	179-181	3	4
β-strand	187-194	8	3
α-helix	198-200	3
β-strand	202-208	7	4
β-strand	215-221	7	4
β-strand	226-229	4	4
β-strand	234	1	3
β-strand	237-242	6	3
β-strand	247-252	6	3
α-helix	257-259	3
β-strand	261-267	7	4
β-strand	279	1	4
β-strand	280	1	3
β-strand	283-287	5	4

Chain D: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	42-45	4	5
β-strand	48-51	4	6
β-strand	57-63	7	5
β-strand	75-80	6	6
β-strand	87-91	5	6
β-strand	95-96	2	6
α-helix	97	1
β-strand	104-109	6	5
β-strand	112-117	6	5
α-helix	122-124	3
β-strand	127-132	6	6
α-helix	138	1
β-strand	140	1	6
β-strand	141	1	5
β-strand	144-148	5	6
β-strand	174-175	2	7
α-helix	176	1
β-strand	179-181	3	8
β-strand	187-192	6	7
β-strand	202-208	7	8
β-strand	215-221	7	8
β-strand	226-229	4	8
β-strand	234	1	7
β-strand	237-242	6	7
β-strand	247-252	6	7
α-helix	257-259	3
β-strand	261-267	7	8
β-strand	278	1	8
β-strand	283-287	5	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CD81 antigen	A, B	protein	99	Homo sapiens	P60033 (AlphaFold model)
Single chain fv fragment	C, D	protein	251	Mus musculus

Sequence of entity 1 (A, B), FASTA

>6EJG_1 CD81 antigen (chains A, B)
GSGFVNKDQIAKDVKQFYDQALQQAVVDDDANNAKAVVKTFHETLDCCGSSTLTALTTSV
LKNNLCPSGSNIISNLFKEDCHQKIDDLFSGKLHHHHHH

Sequence of entity 2 (C, D), FASTA

>6EJG_2 SINGLE CHAIN FV FRAGMENT (chains C, D)
DIVLTQSPASLSVSLGQRATISCRASKSVSTSIYSYMHWYQQKPGQPPKLLIKYASYLES
GVPARFSGSGSGTDFTLNIHPVEEEDAATYYCEHSREFPFTFGTGTKLEIKGGGGSGGGG
SGGGGSGGGGSQVQLQQSGPELVKPGASVKISCKASGYTFSSSWMNWVKQRPGKGLEWIG
RIYSGDGDAIYNGKFKGKATLTADKSSSTAYMQLSSLTSEDSAVYFCAREGKTGDLLLRS
WGQGSALTVSS

Primary citation

Structure-Guided Combinatorial Engineering Facilitates Affinity and Specificity Optimization of Anti-CD81 Antibodies. Nelson, B., Adams, J., Kuglstatter, A. et al. J Mol Biol (2018) 430:2139-2152. DOI 10.1016/j.jmb.2018.05.018 · 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…
5DFV 2.8 Å, Crystal structure of human CD81 large extracellular loop in complex with murine FAB…

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