1YUK: Integrin beta-2 A chain

The crystal structure of the PSI/Hybrid domain/ I-EGF1 segment from the human integrin beta2 at 1.8 resolution. Determined by X-ray diffraction at 1.8 Å resolution. Released 19 Jul 2005.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,906
Mol. weight: 25.31 kDa
Ligands: NDG
Released: 19 Jul 2005

Explore 1YUK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1YUK contains 8 α-helices and 16 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: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	11-15	5
β-strand	22-24	3	1
α-helix	36-39	4
β-strand	40-41	2	1
α-helix	43-48	6
α-helix	53-55	3
β-strand	56-57	2	1
β-strand	62-66	5	2
β-strand	76-77	2	3
β-strand	80-85	6	2
β-strand	91-97	7	3

Chain B: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	344-349	6	2
β-strand	356-363	8	3
α-helix	365-367	3
β-strand	369-373	5	3
β-strand	376-379	4	2
β-strand	387-395	9	3
α-helix	399-401	3
β-strand	402-408	7	2
β-strand	415-421	7	2
α-helix	436-439	4
β-strand	441-444	4	4
β-strand	447-450	4	4
α-helix	451	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin beta-2 A chain	A	protein	103	Homo sapiens	P05107 (AlphaFold model)
Integrin beta-2 B chain	B	protein	120	Homo sapiens	P05107 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1YUK_1 Integrin beta-2 A chain (chains A)
QECTKFKVSSCRECIESGPGCTWCQKLNFTGPGDPDSIRCDTRPQLLMRGCAADDIMDPT
SLAETQEDHNGGQKQLSPQKVTLYLRPGQAAAFNVTFRRAKGY

Sequence of entity 2 (B), FASTA

>1YUK_2 Integrin beta-2 B chain (chains B)
SRVFLDHNALPDTLKVTYDSFCSNGVTHRNQPRGDCDGVQINVPITFQVKVTATECIQEQ
SFVIRALGFTDIVTVQVLPQCECRCRDQSRDRSLCHGKGFLECGICRCDTGYIGKNCEHH

Ligands and cofactors

ID	Name	Formula	Copies
NDG	2-acetamido-2-deoxy-alpha-D-glucopyranose	C8 H15 N O6	2

Primary citation

The Crystal Structure of the Plexin-Semaphorin-Integrin Domain/Hybrid Domain/I-EGF1 Segment from the Human Integrin {beta}2 Subunit at 1.8-A Resolution. Shi, M., Sundramurthy, K., Liu, B. et al. J Biol Chem (2005) 280:30586-30593. DOI 10.1074/jbc.M502525200 · PubMed

Other PDB entries of the same protein (UniProt P05107 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2P26 1.75 Å, Structure of the PHE2 and PHE3 fragments of the integrin beta2 subunit
5E6X 1.75 Å, Re-refinement of the Crystal Structure of the Plexin-Semaphorin-Integrin Domain/Hybrid…
5E6V 1.8 Å, Re-refinement of the Crystal Structure of the Plexin-Semaphorin-Integrin Domain/Hybrid…
5E6S 2.15 Å, Structures of leukocyte integrin aLB2: The aI domain, the headpiece, and the pocket for…
2JF1 2.2 Å, Crystal structure of the filamin a repeat 21 complexed with the integrin BETA2…
2P28 2.2 Å, Structure of the PHE2 and PHE3 fragments of the integrin beta2 subunit
5E6W 2.2 Å, Re-refinement of the Crystal Structure of the Plexin-Semaphorin-Integrin Domain/Hybrid…
2V7D 2.5 Å, 14-3-3 protein zeta in complex with Thr758 phosphorylated integrin beta2 peptide
5E6U 2.5 Å, Structures of leukocyte integrin aLb2: The aI domain, the headpiece, and the pocket for…
9RM9 2.6 Å, Cryo-EM structure of alphaM/beta2 headpiece complex without alphaM I-domain - the…
7USL 2.7 Å, Integrin alphaM/beta2 ectodomain in complex with adenylate cyclase toxin RTX751 and M1F5…
7USM 2.7 Å, Integrin alphaM/beta2 ectodomain

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