6EJM: Human CD81 large extracellular loop

Crystal structure of human CD81 large extracellular loop in complex with single chain fv fragment 5. Determined by X-ray diffraction at 2.15 Å resolution. Released 30 May 2018.

Method: X-ray diffraction
Resolution: 2.15 Å
Organisms: Homo sapiens, Mus musculus
Chains: 4
Atoms: 5,072
Mol. weight: 73.84 kDa
Released: 30 May 2018

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

Secondary structure: helices and β-sheets

6EJM contains 21 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: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	116-134	19
α-helix	141-153	13
α-helix	163-170	8
α-helix	190-198	9

Chain B: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	116-136	21
α-helix	142-150	9
α-helix	151-155	5
α-helix	160-162	3
α-helix	163-167	5
α-helix	169-172	4
α-helix	190-198	9

Chain H: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	41-45	5	1
β-strand	48-50	3	2
β-strand	56-63	8	1
α-helix	67-69	3
β-strand	72-77	6	2
β-strand	83-89	7	2
β-strand	96-97	2	2
β-strand	107-111	5	1
α-helix	112-114	3
β-strand	116-121	6	1
α-helix	126-128	3
β-strand	130-135	6	2
β-strand	144	1	2
β-strand	148-152	5	2
β-strand	178-181	4	3
β-strand	184-187	4	4
β-strand	193-199	7	3
β-strand	204	1	5
β-strand	210	1	5
β-strand	212-217	6	4
β-strand	223-228	6	4
β-strand	232-233	2	4
α-helix	234	1
β-strand	241-246	6	3
β-strand	249-254	6	3
α-helix	259-261	3
β-strand	263-269	7	4
α-helix	275	1
β-strand	276-277	2	4
β-strand	281-285	5	4

Chain I: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	41-45	5	6
β-strand	48-50	3	7
β-strand	56-63	8	6
α-helix	67-69	3
β-strand	72-77	6	7
β-strand	83-89	7	7
β-strand	96-97	2	7
β-strand	107-111	5	6
β-strand	116-121	6	6
α-helix	126-128	3
β-strand	130-135	6	7
β-strand	144	1	7
β-strand	148-152	5	7
β-strand	178-181	4	8
β-strand	184-187	4	9
β-strand	193-199	7	8
β-strand	204	1	10
β-strand	210	1	10
β-strand	212-217	6	9
α-helix	222	1
β-strand	223-228	6	9
β-strand	232-233	2	9
β-strand	241-246	6	8
β-strand	249-254	6	8
β-strand	264-269	6	9
α-helix	275	1
β-strand	276-277	2	9
β-strand	281-285	5	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CD81 antigen	A, B	protein	99	Homo sapiens	P60033 (AlphaFold model)
Single chain fv fragment	H, I	protein	249	Mus musculus

Sequence of entity 1 (A, B), FASTA

>6EJM_1 CD81 antigen (chains A, B)
GSGFVNKDQIAKDVKQFYDQALQQAVVDDDANNAKAVVKTFHETLDCCGSSTLTALTTSV
LKNNLCPSGSNIISNLFKEDCHQKIDDLFSGKLHHHHHH

Sequence of entity 2 (H, I), FASTA

>6EJM_2 SINGLE CHAIN FV FRAGMENT (chains H, I)
AEVMLVESGGGFVKPGGSLKLSCAASGFTFRSYIMSWVRQTPEKRLEWVATISGGGGNTY
YPDSVKGRFTISRDNAKNTLYLQLSSLRSEDTALYYCASLTAVGDYWGQGTSVTVSSGGG
GSGGGGSGGGGSGGGGSDVVMTQTPLTLSVTIGQPASISCKSSQSLFDTDGKTYLTWLLQ
RPGQSPKRLIYLVSKLASGVPDRFTGSGSGTDFTLKISRVEAEDLGVYYCLQGTHFPLTF
GAGTKLDLK

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

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