6RHW: Human CD11b I-domain

Crystal structure of human CD11b I-domain (CD11b-I) in complex with Staphylococcus aureus octameric bi-component leukocidin LukGH. Determined by X-ray diffraction at 2.75 Å resolution. Released 18 Dec 2019.

Method
X-ray diffraction
Resolution
2.75 Å
Organisms
Staphylococcus aureus, Homo sapiens
Chains
3
Atoms
5,757
Mol. weight
96.09 kDa
Ligands
MG
Released
18 Dec 2019

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

Secondary structure: helices and β-sheets

6RHW contains 18 α-helices and 49 β-strands across 3 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 C: 10 helices, 8 β-strands

ElementResiduesLengthSheet
β-strand133-140810
α-helix147-16317
β-strand169-176810
β-strand180-184510
α-helix186-1916
α-helix195-1995
β-strand209111
α-helix211-2177
α-helix218-2225
β-strand234-241810
β-strand246111
α-helix252-2543
α-helix256-2616
β-strand264-270710
α-helix279-2879
α-helix2891
α-helix293-2953
β-strand296-298310
Chain G: 4 helices, 21 β-strands
ElementResiduesLengthSheet
β-strand19-29111
β-strand34-44111
β-strand51-5771
β-strand60-6231
β-strand66-6722
β-strand75-90162
β-strand97-10371
β-strand112-12093
β-strand138-151143
β-strand153-15752
β-strand165-17282
β-strand175-17734
β-strand180-18234
β-strand19512
β-strand20015
α-helix209-2113
β-strand21315
α-helix214-2152
α-helix216-2183
α-helix221-2244
β-strand226-22721
β-strand231-23771
β-strand244-263202
β-strand270-291222
β-strand296-30272
Chain H: 4 helices, 20 β-strands
ElementResiduesLengthSheet
β-strand46-55106
β-strand60-69106
β-strand7411
β-strand77-88126
β-strand92-9547
β-strand103-118167
β-strand123-12976
β-strand136-149143
β-strand161-170103
β-strand176-18057
β-strand188-19587
β-strand197-20048
β-strand203-20648
β-strand21419
α-helix225-2284
β-strand22919
α-helix232-2343
α-helix237-2404
β-strand242-24326
β-strand247-25376
β-strand259-275177
α-helix282-2843
β-strand285-302187
β-strand307-317117

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Beta-channel forming cytolysinGprotein309Staphylococcus aureusQ2FWP0 (AlphaFold model)
Beta-channel forming cytolysinHprotein324Staphylococcus aureusQ2FWN9 (AlphaFold model)
Integrin alpha-MCprotein195Homo sapiensP11215 (AlphaFold model)
Sequence of entity 1 (G), FASTA
>6RHW_1 Beta-channel forming cytolysin (chains G)
KINSEIKQVSEKNLDGDTKMYTRTATTSDSQKNITQSLQFNFLTEPNYDKETVFIKAKGT
IGSGLRILDPNGYWNSTLRWPGSYSVSIQNVDDNNNTNVTDFAPKNQDESREVKYTYGYK
TGGDFSINRGGLTGNITKESNYSETISYQQPSYRTLLDQSTSHKGVGWKVEAHLINNMGH
DHTRQLTNDSDNRTKSEIFSLTRNGNLWAKDNFTPKDKMPVTVSEGFNPEFLAVMSHDKK
DKGKSQFVVHYKRSMDEFKIDWNRHGFWGYWSGENHVDKKEEKLSALYEVDWKTHNVKFV
KVLNDNEKK
Sequence of entity 2 (H), FASTA
>6RHW_2 Beta-channel forming cytolysin (chains H)
NSAHKDSQDQNKKEHVDKSQQKDKRNVTNKDKNSTAPDDIGKNGKITKRTETVYDEKTNI
LQNLQFDFIDDPTYDKNVLLVKKQGSIHSNLKFESHKEEKNSNWLKYPSEYHVDFQVKRN
RKTEILDQLPKNKISTAKVDSTFSYSSGGKFDSTKGIGRTSSNSYSKTISYNQQNYDTIA
SGKNNNWHVHWSVIANDLKYGGEVKNRNDELLFYRNTRIATVENPELSFASKYRYPALVR
SGFNPEFLTYLSNEKSNEKTQFEVTYTRNQDILKNRPGIHYAPPILEKNKDGQRLIVTYE
VDWKNKTVKVVDKYSDDNKPYKEG
Sequence of entity 3 (C), FASTA
>6RHW_3 Integrin alpha-M (chains C)
GCPQEDSDIAFLIDGSGSIIPHDFRRMKEFVSTVMEQLKKSKTLFSLMQYSEEFRIHFTF
KEFQNNPNPRSLVKPITQLLGRTHTATGIRKVVRELFNITNGARKNAFKILVVITDGEKF
GDPLGYEDVIPEADREGVIRYVIGVGDAFRSEKSRQELNTIASKPPRDHVFQVNNFEALK
TIQNQLREKIFAIEG

Ligands and cofactors

IDNameFormulaCopies
MGMagnesium ionMg1

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

Primary citation

Molecular mechanism of leukocidin GH-integrin CD11b/CD18 recognition and species specificity. Trstenjak, N., Milic, D., Graewert, M.A. et al. Proc Natl Acad Sci U S A (2020) 117:317-327. DOI 10.1073/pnas.1913690116 · PubMed

Other PDB entries of the same protein (UniProt Q2FWP0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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