6BXB: Extended b3 integrin P33

Crystal structure of an extended b3 integrin P33. Determined by X-ray diffraction at 2.39 Å resolution. Released 1 Aug 2018.

Method: X-ray diffraction
Resolution: 2.39 Å
Organism: Homo sapiens
Chains: 2
Atoms: 7,469
Mol. weight: 105.26 kDa
Ligands: MG, NAG, CA
Released: 1 Aug 2018

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

Secondary structure: helices and β-sheets

6BXB contains 43 α-helices and 60 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: 24 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
α-helix	13-17	5
β-strand	24-25	2	1
β-strand	38-39	2	1
α-helix	41-46	6
α-helix	51-53	3
β-strand	55	1	1
β-strand	60-65	6	2
α-helix	67-71	5
β-strand	83-84	2	3
β-strand	87-92	6	2
β-strand	97-105	9	3
β-strand	112-119	8	4
β-strand	121	1	5
α-helix	126-142	17
β-strand	148-155	8	4
β-strand	159-163	5	4
α-helix	165-171	7
α-helix	174-177	4
β-strand	186	1	5
α-helix	190-200	11
α-helix	204-206	3
β-strand	213-220	8	4
α-helix	231-233	3
β-strand	237-243	7	4
α-helix	245-247	3
α-helix	250-254	5
α-helix	257-259	3
α-helix	261	1
α-helix	263	1
α-helix	264-267	4
β-strand	268-271	4	4
α-helix	277-284	8
α-helix	285-287	3
β-strand	291-293	3	6
β-strand	294-297	4	2
β-strand	303-310	8	3
β-strand	316-318	3	3
β-strand	322-324	3	6
β-strand	331-340	10	3
β-strand	348-355	8	2
β-strand	362-368	7	2
α-helix	373-375	3
β-strand	390-393	4	7
β-strand	396-399	4	7
α-helix	420-422	3
α-helix	430	1
α-helix	431-434	4
β-strand	436-439	4	8
β-strand	442-445	4	8
α-helix	446-447	2
β-strand	452-454	3	9
β-strand	460-462	3	9

Chain B: 19 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	13-19	7
β-strand	24-26	3	10
β-strand	38-39	2	10
α-helix	41-46	6
α-helix	51-53	3
β-strand	54-55	2	10
β-strand	60-65	6	11
α-helix	67-70	4
β-strand	83-84	2	12
β-strand	87-92	6	11
β-strand	97-105	9	12
β-strand	112-119	8	13
β-strand	121	1	14
α-helix	126-142	17
β-strand	148-155	8	13
β-strand	159-160	2	13
α-helix	165-171	7
α-helix	174-178	5
β-strand	186	1	14
α-helix	190-199	10
β-strand	213-220	8	13
β-strand	241-243	3	13
α-helix	245-247	3
α-helix	250-254	5
α-helix	261	1
α-helix	263	1
β-strand	269-271	3	13
α-helix	275-277	3
α-helix	280-282	3
α-helix	284-289	6
β-strand	291-293	3	15
β-strand	294-297	4	11
β-strand	303-310	8	12
β-strand	316-318	3	12
β-strand	322-324	3	15
β-strand	331-340	10	12
β-strand	348-355	8	11
β-strand	362-368	7	11
α-helix	373-375	3
β-strand	390-393	4	16
β-strand	396-399	4	16
β-strand	404	1	17
β-strand	410	1	17
α-helix	430	1
α-helix	431-434	4
β-strand	436-438	3	18
β-strand	443-445	3	18
α-helix	446-447	2
β-strand	451-454	4	19
β-strand	460-463	4	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chimera protein of Integrin beta-3 and Integrin alpha-L	A, B	protein	466	Homo sapiens	P05106 (AlphaFold model), P20701 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6BXB_1 Chimera protein of Integrin beta-3 and Integrin alpha-L (chains A, B)
GPNICTTRGVSSCQQCLAVSPMCAWCSDEALPPGSPRCDLKENLLKDNCAPESIEFPVSE
ARVLEDRPLSDKGSGDSSQVTQVSPQRIALRLRPDDSKNFSIQVRQVEDGNVDLVFLFDG
SMSLQPDEFQKILDFMKDVMKKLSNTSYQFAAVQFSTSYKTEFDFSDYVKWKDPDALLKH
VKHMLLLTNTFGAINYVATEVFREELGARPDATKVLIIITDGEATDSGNIDAAKDIIRYI
IGIGKHFQTKESQETLHKFASKPASEFVKILDTFEKLKDLFTELQKKIRSKVELEVRDLP
EELSLSFNATCLNNEVIPGLKSCMGLKIGDTVSFSIEAKVRGCPQEKEKSFTIKPVGFKD
SLIVQVTFDCDCACQAQAEPNSHRCNNGNGTFECGVCRCGPGWLGSQCECSEEDYRPSQQ
DECSPREGQPVCSQRGECLCGQCVCHSSDFGKITGKYCETRELYFQ

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5
CA	Calcium ion	Ca	1

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

Primary citation

Structure of an extended beta3integrin. Zhou, D., Thinn, A.M.M., Zhao, Y. et al. Blood (2018) 132:962-972. DOI 10.1182/blood-2018-01-829572 · PubMed

Other PDB entries of the same protein (UniProt P05106 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1MIZ 1.9 Å, Crystal structure of an integrin beta3-talin chimera
7UDH 2.0 Å, Integrin alpha IIB beta3 complex with BMS4-3
4HXJ 2.0 Å, Crystal structure of SH3:RGT complex
7UBR 2.05 Å, Integrin alpha IIB beta3 complex with GR144053
6BXJ 2.09 Å, Structure of a single-chain beta3 integrin
1MK7 2.2 Å, Crystal structure of an integrin BETA3-talin chimera
3T3P 2.2 Å, A Novel High Affinity Integrin alphaIIbbeta3 Receptor Antagonist That Unexpectedly…
7TMZ 2.2 Å, Integrin alpha IIB beta3 complex with BMS compound 4
2Q6W 2.25 Å, The structure of HLA-DRA, DRB3*0101 (DR52a) with bound platelet integrin peptide…
3NIG 2.25 Å, The Closed Headpiece of Integrin IIb 3 and its Complex with an IIb 3 -Specific…
7U9V 2.25 Å, Integrin alpha IIB beta3 complex with BMS4-1
3NID 2.3 Å, The Closed Headpiece of Integrin alphaIIB beta3 and its Complex with an alpahIIB beta3…

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