5DFW: Human CD81 large extracellular loop

Crystal structure of human CD81 large extracellular loop in complex with single chain fv fragment K13. Determined by X-ray diffraction at 2.33 Å resolution. Released 16 Dec 2015.

Method: X-ray diffraction
Resolution: 2.33 Å
Organisms: Homo sapiens, Mus musculus
Chains: 2
Atoms: 2,501
Mol. weight: 36.66 kDa
Released: 16 Dec 2015

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

Secondary structure: helices and β-sheets

5DFW contains 16 α-helices and 22 β-strands across 2 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, 0 β-strands

Element	Residues	Length
α-helix	116-134	19
α-helix	142-154	13
α-helix	160-165	6
α-helix	166-171	6
α-helix	176	1
α-helix	181-185	5
α-helix	187-189	3
α-helix	190-199	10

Chain H: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	105-106	2	1
α-helix	107-109	3
β-strand	110-112	3	2
β-strand	118-123	6	1
α-helix	154-156	3
β-strand	197-204	7	2
β-strand	210-253	8	2
β-strand	291-293	3	2
α-helix	295-297	3
β-strand	303-307	5	1
β-strand	312-317	6	1
α-helix	322-324	3
β-strand	326-352	9	2
β-strand	396-397	2	2
α-helix	399-402	3
β-strand	405-409	5	2
β-strand	504-507	4	3
β-strand	510-512	3	4
β-strand	519-552	7	3
β-strand	598-604	6	4
α-helix	609-610	2
β-strand	611-615	5	4
β-strand	696-697	2	4
α-helix	698	1
β-strand	706-711	6	3
β-strand	716-721	6	3
α-helix	726-728	3
β-strand	730-752	7	4
β-strand	801	1	4
β-strand	805-808	4	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CD81 antigen	A	protein	98	Homo sapiens	P60033 (AlphaFold model)
Single chain fv fragment	H	protein	243	Mus musculus

Sequence of entity 1 (A), FASTA

>5DFW_1 CD81 antigen (chains A)
GSGFVNKDQIAKDVKQFYDQALQQAVVDDDANNAKAVVKTFHETLDCCGSSTLTALTTSV
LKNNLCPSGSNIISNLFKEDCHQKIDDLFSGKHHHHHH

Sequence of entity 2 (H), FASTA

>5DFW_2 SINGLE CHAIN FV FRAGMENT (chains H)
EVRLHQSAAQLVQPGASVRLSCTTSGFNFKDSYLHWVKQRPAQGLEWIGRIDTGNGNVKF
DPKFQDKATITTDIPSMTAYLHLSNLTSEDTAVYYCVPYGYGFHSWGDGTTLTVSSGGGG
SGGGGSGGGGSGGGGSDIQMTQSPASLSVSVGETVTITCRASENIYRTLAWYLQKQGKSP
QLLVYGATTLADGVPSRFSGSGSGTQYYLKINSLQSEDFGTYHCQHFWGTPWTFGGGTKV
EIK

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…
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…
6EJG 2.82 Å, Crystal structure of human CD81 large extracellular loop in complex with single chain fv…

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