6U9S: Human CD81 large extracellular loop

Crystal structure of human CD81 large extracellular loop in complex with 5A6 Fab. Determined by X-ray diffraction at 2.4 Å resolution. Released 13 May 2020.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Mus musculus, Homo sapiens
Chains: 6
Atoms: 8,350
Mol. weight: 119.6 kDa
Released: 13 May 2020

Explore 6U9S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6U9S contains 42 α-helices and 92 β-strands across 6 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, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
β-strand	10-12	3	2
β-strand	18-25	8	1
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	58-60	3	2
α-helix	62-64	3
β-strand	68-73	6	1
α-helix	74-76	3
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-100	9	2
β-strand	105-109	5	2
β-strand	110	1	1
β-strand	113-117	5	2
β-strand	123	1	3
β-strand	126-130	5	4
β-strand	137-138	2	4
β-strand	141-151	11	4
β-strand	152	1	3
β-strand	157-160	4	5
β-strand	169-171	3	4
α-helix	172-174	3
β-strand	175-176	2	4
β-strand	182-191	10	4
α-helix	192-194	3
β-strand	201-206	6	5
α-helix	207-209	3
β-strand	211-216	6	5
α-helix	218-220	3

Chain B: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-13	4	7
β-strand	19-25	7	6
β-strand	30	1	8
β-strand	37	1	8
β-strand	39-44	6	7
β-strand	51-55	5	7
β-strand	59-60	2	7
α-helix	61	1
β-strand	68-73	6	6
β-strand	76-81	6	6
α-helix	86-88	3
β-strand	90-96	7	7
β-strand	102-103	2	7
β-strand	107-111	5	7
β-strand	116	1	9
α-helix	117-118	2
β-strand	119-123	5	10
α-helix	124-126	3
α-helix	127-130	4
β-strand	134-144	11	10
β-strand	145	1	9
β-strand	149-155	7	11
β-strand	158-159	2	11
β-strand	164-168	5	10
α-helix	169-172	4
β-strand	178-187	10	10
α-helix	188-192	5
β-strand	196-203	8	11
β-strand	210-215	6	11

Chain C: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	113-115	3
α-helix	116-136	21
α-helix	141-154	14
α-helix	163-165	3
α-helix	166-171	6
α-helix	182-184	3
α-helix	187-189	3
α-helix	190-198	9

Chain D: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	12
β-strand	10-12	3	13
β-strand	18-25	8	12
β-strand	34-39	6	13
β-strand	45-51	7	13
β-strand	58-60	3	13
α-helix	62-64	3
β-strand	68-73	6	12
α-helix	74-76	3
β-strand	78-83	6	12
α-helix	88-90	3
β-strand	92-100	9	13
β-strand	105-109	5	13
β-strand	110	1	12
β-strand	113-117	5	13
β-strand	123	1	14
β-strand	126-130	5	15
β-strand	137-138	2	15
β-strand	141-151	11	15
β-strand	152	1	14
β-strand	157-160	4	16
β-strand	169-171	3	15
α-helix	172-174	3
β-strand	175-176	2	15
β-strand	182-191	10	15
α-helix	192-194	3
β-strand	201-206	6	16
α-helix	207-209	3
β-strand	211-216	6	16

Chain E: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	17
β-strand	10-13	4	18
β-strand	19-25	7	17
β-strand	30	1	19
β-strand	37	1	19
β-strand	39-44	6	18
β-strand	50-55	6	18
β-strand	59-60	2	18
α-helix	61	1
β-strand	68-73	6	17
β-strand	76-81	6	17
α-helix	86-88	3
β-strand	90-96	7	18
β-strand	102-103	2	18
β-strand	107-111	5	18
β-strand	116	1	20
α-helix	117-118	2
β-strand	119-123	5	21
α-helix	124-126	3
α-helix	127-130	4
β-strand	134-144	11	21
β-strand	145	1	20
β-strand	149-155	7	22
β-strand	158-159	2	22
β-strand	164-168	5	21
α-helix	169-172	4
β-strand	178-187	10	21
α-helix	188-191	4
β-strand	196-203	8	22
β-strand	210-215	6	22

Chain F: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	116-136	21
α-helix	142-154	13
α-helix	163-165	3
α-helix	166-171	6
α-helix	182-185	4
α-helix	187-189	3
α-helix	190-199	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5A6 FAB Heavy Chain	A, D	protein	232	Mus musculus
5A6 FAB Light Chain	B, E	protein	219	Mus musculus
CD81 antigen	C, F	protein	98	Homo sapiens	P60033 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>6U9S_1 5A6 FAB Heavy Chain (chains A, D)
QVQLVQSGSELKKPGASVKVSCKASGYTFTDDSIHWVRQAPGQGLEWMGWINTETGEPTY
ADDFKGRFVFSLDTSVSTAYLQISSLKAEDTAVYYCARLSPVVVIFIYWGQGTLVTVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGGSGLEVLFQ

Sequence of entity 2 (B, E), FASTA

>6U9S_2 5A6 FAB Light Chain (chains B, E)
DIVMTQSPLSLPVTPGEPASISCKSSQSLLHSRTRKNYLAWYLQKPGQSPQLLIYWASTR
ESGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCKQSYNLYAFGQGTKLEIKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (C, F), FASTA

>6U9S_3 CD81 antigen (chains C, F)
ETGFVNKDQIAKDVKQFYDQALQQAVVDDDANNAKAVVKTFHETLDCCGSSTLTALTTSV
LKNNLCPSGSNIISNLFKEDCHQKIDDLFSGSHHHHHH

Primary citation

A dynamic interaction between CD19 and the tetraspanin CD81 controls B cell co-receptor trafficking. Susa, K.J., Seegar, T.C., Blacklow, S.C. et al. Elife (2020) 9. DOI 10.7554/eLife.52337 · 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)
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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