5M3D: Structural tuning of CD81LEL

Structural tuning of CD81LEL (space group P31). Determined by X-ray diffraction at 2.38 Å resolution. Released 14 Dec 2016.

Method: X-ray diffraction
Resolution: 2.38 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,794
Mol. weight: 45.67 kDa
Ligands: PO4
Released: 14 Dec 2016

Explore 5M3D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5M3D contains 29 α-helices and 0 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: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	116-136	21
α-helix	141-154	14
α-helix	161-170	10
α-helix	172-174	3
α-helix	176	1
α-helix	181-185	5
α-helix	188-189	2
α-helix	190-199	10

Chain B: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	116-136	21
α-helix	141-154	14
α-helix	161-170	10
α-helix	172-174	3
α-helix	176	1
α-helix	183-186	4
α-helix	190-199	10

Chain C: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	116-134	19
α-helix	143-154	12
α-helix	161-170	10
α-helix	172-174	3
α-helix	182-185	4
α-helix	190-199	10

Chain D: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	116-135	20
α-helix	143-154	12
α-helix	161-170	10
α-helix	172-174	3
α-helix	176	1
α-helix	182-185	4
α-helix	188-189	2
α-helix	190-199	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CD81 antigen	A, B, C, D	protein	101	Homo sapiens	P60033 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>5M3D_1 CD81 antigen (chains A, B, C, D)
ETGFVNKDQIAKDVKQFYDQALQQAVVDDDANNAKAVVKTFHETLDCCGSSTLTALTTSV
LKNNLCPSGSNIISNLFKEDCHQKIDDLFSGKGTKHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	6

Water and common crystallization additives (EDO) are not listed.

Primary citation

Mechanism of Structural Tuning of the Hepatitis C Virus Human Cellular Receptor CD81 Large Extracellular Loop. Cunha, E.S., Sfriso, P., Rojas, A.L. et al. Structure (2017) 25:53-65. DOI 10.1016/j.str.2016.11.003 · 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…
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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