6RHV: Mouse CD11b I-domain

Crystal structure of mouse CD11b I-domain (CD11b-I) in complex with Staphylococcus aureus octameric bi-component leukocidin LukGH (LukH K319A mutant). Determined by X-ray diffraction at 2.29 Å resolution. Released 18 Dec 2019.

Method
X-ray diffraction
Resolution
2.29 Å
Organisms
Staphylococcus aureus, Mus musculus
Chains
3
Atoms
6,425
Mol. weight
95.89 kDa
Ligands
MG
Released
18 Dec 2019

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

Secondary structure: helices and β-sheets

6RHV contains 18 α-helices and 53 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-strand133-140812
α-helix147-16317
β-strand170-176712
β-strand180-184512
α-helix186-1916
α-helix195-1995
β-strand209113
α-helix211-2177
α-helix218-2225
α-helix225-2273
β-strand234-241812
β-strand246113
α-helix252-26110
β-strand264-270712
α-helix278-28710
α-helix2891
α-helix292-2943
β-strand296-298312
Chain G: 4 helices, 24 β-strands
ElementResiduesLengthSheet
β-strand19-29111
β-strand34-44111
β-strand50-5781
β-strand60-6231
β-strand66-6722
β-strand75-90162
β-strand97-10371
β-strand112-122113
β-strand125-12624
β-strand133-13424
β-strand13515
β-strand137-151153
β-strand153-15752
β-strand165-17282
β-strand175-17736
β-strand180-18236
β-strand19512
β-strand20017
α-helix209-2113
β-strand21317
α-helix214-2152
α-helix216-2183
α-helix221-2244
β-strand226-22721
β-strand231-23881
β-strand244-265222
β-strand268-291242
β-strand296-30272
Chain H: 4 helices, 21 β-strands
ElementResiduesLengthSheet
α-helix38-392
β-strand45-55118
β-strand60-70118
β-strand7411
β-strand76-88138
β-strand92-9549
β-strand103-118169
β-strand123-12978
β-strand136-149143
β-strand15215
β-strand160-170113
β-strand176-18059
β-strand188-19589
β-strand197-200410
β-strand203-206410
β-strand214111
α-helix225-2284
β-strand229111
α-helix232-2343
α-helix237-2404
β-strand242-24328
β-strand247-25488
β-strand259-275179
β-strand285-302189
β-strand307-316109

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Beta-channel forming cytolysinGprotein309Staphylococcus aureusQ2FWP0 (AlphaFold model)
Beta-channel forming cytolysinHprotein324Staphylococcus aureusQ2FWN9 (AlphaFold model)
Integrin alpha-MCprotein195Mus musculusP05555 (AlphaFold model)
Sequence of entity 1 (G), FASTA
>6RHV_1 Beta-channel forming cytolysin (chains G)
KINSEIKQVSEKNLDGDTKMYTRTATTSDSQKNITQSLQFNFLTEPNYDKETVFIKAKGT
IGSGLRILDPNGYWNSTLRWPGSYSVSIQNVDDNNNTNVTDFAPKNQDESREVKYTYGYK
TGGDFSINRGGLTGNITKESNYSETISYQQPSYRTLLDQSTSHKGVGWKVEAHLINNMGH
DHTRQLTNDSDNRTKSEIFSLTRNGNLWAKDNFTPKDKMPVTVSEGFNPEFLAVMSHDKK
DKGKSQFVVHYKRSMDEFKIDWNRHGFWGYWSGENHVDKKEEKLSALYEVDWKTHNVKFV
KVLNDNEKK
Sequence of entity 2 (H), FASTA
>6RHV_2 Beta-channel forming cytolysin (chains H)
NSAHKDSQDQNKKEHVDKSQQKDKRNVTNKDKNSTAPDDIGKNGKITKRTETVYDEKTNI
LQNLQFDFIDDPTYDKNVLLVKKQGSIHSNLKFESHKEEKNSNWLKYPSEYHVDFQVKRN
RKTEILDQLPKNKISTAKVDSTFSYSSGGKFDSTKGIGRTSSNSYSKTISYNQQNYDTIA
SGKNNNWHVHWSVIANDLKYGGEVKNRNDELLFYRNTRIATVENPELSFASKYRYPALVR
SGFNPEFLTYLSNEKSNEKTQFEVTYTRNQDILKNRPGIHYAPPILEKNKDGQRLIVTYE
VDWKNKTVKVVDKYSDDNAPYKEG
Sequence of entity 3 (C), FASTA
>6RHV_3 Integrin alpha-M (chains C)
ECPQQESDIVFLIDGSGSINNIDFQKMKEFVSTVMEQFKKSKTLFSLMQYSDEFRIHFTF
NDFKRNPSPRSHVSPIKQLNGRTKTASGIRKVVRELFHKTNGARENAAKILVVITDGEKF
GDPLDYKDVIPEADRAGVIRYVIGVGNAFNKPQSRRELDTIASKPAGEHVFQVDNFEALN
TIQNQLQEKIFAIEG

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:

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