6EK2: Human CD81 large extracellular loop

Crystal structure of human CD81 large extracellular loop in complex with single chain fv fragment 10. Determined by X-ray diffraction at 2.65 Å resolution. Released 30 May 2018.

Method: X-ray diffraction
Resolution: 2.65 Å
Organisms: Homo sapiens, Mus musculus
Chains: 4
Atoms: 5,162
Mol. weight: 74.35 kDa
Released: 30 May 2018

Explore 6EK2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6EK2 contains 20 α-helices and 50 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: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	116-136	21
α-helix	141-154	14
α-helix	163-165	3
α-helix	166-171	6
β-strand	181-182	2	1
β-strand	185-186	2	1
α-helix	190-199	10

Chain B: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	116-135	20
α-helix	141-154	14
α-helix	163-165	3
α-helix	166-171	6
β-strand	181-182	2	2
β-strand	185-186	2	2
α-helix	190-199	10

Chain H: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	172-176	5	3
β-strand	180-181	2	4
β-strand	187-194	8	3
α-helix	198-200	3
β-strand	203-208	6	5
β-strand	214-220	7	5
β-strand	227-229	3	5
β-strand	237-242	6	3
β-strand	247-252	6	3
α-helix	257-259	3
β-strand	261-268	8	5
β-strand	276-279	4	5
β-strand	283-285	3	5
β-strand	286-287	2	4
β-strand	342-343	2	6
β-strand	348-350	3	7
β-strand	357-363	7	6
β-strand	371-376	6	7
α-helix	381-382	2
β-strand	383-387	5	7
β-strand	391-392	2	7
α-helix	393	1
β-strand	400-405	6	6
β-strand	408-413	6	6
α-helix	418-420	3
β-strand	423-428	6	7
β-strand	436	1	7
β-strand	440-443	4	7

Chain I: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	172-176	5	8
β-strand	181	1	9
β-strand	187-194	8	8
α-helix	198-200	3
β-strand	203-208	6	10
β-strand	214-220	7	10
β-strand	227-229	3	10
β-strand	237-242	6	8
β-strand	247-252	6	8
α-helix	257-259	3
β-strand	261-268	8	10
β-strand	276-279	4	10
β-strand	283-285	3	10
β-strand	287	1	9
β-strand	342-343	2	11
β-strand	348-350	3	12
β-strand	357-363	7	11
β-strand	371-376	6	12
α-helix	381-382	2
β-strand	383-387	5	12
β-strand	391-392	2	12
α-helix	393	1
β-strand	400-405	6	11
β-strand	408-413	6	11
α-helix	418-420	3
β-strand	423-428	6	12
β-strand	436	1	12
β-strand	440-443	4	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CD81 antigen	A, B	protein	98	Homo sapiens	P60033 (AlphaFold model)
Single chain fv fragment	H, I	protein	247	Mus musculus

Sequence of entity 1 (A, B), FASTA

>6EK2_1 CD81 antigen (chains A, B)
GSGFVNKDQIAKDVKQFYDQALQQAVVDDDANNAKAVVKTFHETLDCCGSSTLTALTTSV
LKNNLCPSGSNIISNLFKEDCHQKIDDLFSGKHHHHHH

Sequence of entity 2 (H, I), FASTA

>6EK2_2 SINGLE CHAIN FV FRAGMENT (chains H, I)
EVQLVESGGGLVKPGGSLKLSCAASGFTFSDYYMHWVRQTPKKRLEWVATISDGGSYTYF
LDSVKGRFTISRDNAKNKLDLQMSSLKSEDTGMYYCARDGNKYSAWFAYWGQGTLVTVSA
GGGGSGGGGSGGGGSGGGGSDIQMTQSSSSFSVSLGDRVTITCKASEDIYNRLAWYQQKP
GNAPRLLISGATSLETGVPSRFSGSGSGKDYTLSITSLQTEDFATYYCQQYWSPPWTFGG
GTKLEIK

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.
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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