4M76: Integrin I domain of complement receptor 3

Integrin I domain of complement receptor 3 in complex with C3d. Determined by X-ray diffraction at 2.8 Å resolution. Released 2 Oct 2013.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,804
Mol. weight: 55.8 kDa
Ligands: NI
Released: 2 Oct 2013

Explore 4M76 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4M76 contains 28 α-helices and 14 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: 16 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	993-996	4
α-helix	997-1003	7
α-helix	1013-1031	19
α-helix	1040-1057	18
β-strand	1060	1	1
β-strand	1066	1	1
α-helix	1073-1075	3
α-helix	1076-1088	13
α-helix	1097-1111	15
β-strand	1112	1	2
β-strand	1118	1	2
α-helix	1127-1129	3
α-helix	1131-1133	3
α-helix	1140-1152	13
α-helix	1165-1179	15
α-helix	1186-1197	12
α-helix	1205-1212	8
β-strand	1215	1	3
β-strand	1219	1	3
α-helix	1226-1242	17
α-helix	1249-1257	9
α-helix	1269-1285	17

Chain B: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	133-140	8	4
α-helix	147-162	16
β-strand	169-176	8	4
β-strand	180-184	5	4
α-helix	186-191	6
α-helix	195-199	5
β-strand	209	1	5
α-helix	211-217	7
α-helix	218-222	5
α-helix	225-227	3
α-helix	229-230	2
β-strand	234-240	7	4
β-strand	246	1	5
α-helix	252-254	3
α-helix	256-261	6
β-strand	265-270	6	4
α-helix	279-287	9
α-helix	292-294	3
β-strand	296-298	3	4
α-helix	302-304	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Complement C3	A	protein	298	Homo sapiens	P01024 (AlphaFold model)
Integrin alpha-M	B	protein	198	Homo sapiens	P11215 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4M76_1 Complement C3 (chains A)
GAMAVDAERLKHLIVTPSGAGEQNMIGMTPTVIAVHYLDETEQWEKFGLEKRQGALELIK
KGYTQQLAFRQPSSAFAAFVKRAPSTWLTAYVVKVFSLAVNLIAIDSQVLCGAVKWLILE
KQKPDGVFQEDAPVIHQEMIGGLRNNNEKDMALTAFVLISLQEAKDICEEQVNSLPGSIT
KAGDFLEANYMNLQRSYTVAIAGYALAQMGRLKGPLLNKFLTTAKDKNRWEDPGKQLYNV
EATSYALLALLQLKDFDFVPPVVRWLNEQRYYGGGYGSTQATFMVFQALAQYQKDAPD

Sequence of entity 2 (B), FASTA

>4M76_2 Integrin alpha-M (chains B)
GAMGSPQEDSDIAFLIDGSGSIIPHDFRRMKEFVSTVMEQLKKSKTLFSLMQYSEEFRIH
FTFKEFQNNPNPRSLVKPITQLLGRTHTATGIRKVVRELFNITNGARKNAFKILVVITDG
EKFGDPLGYEDVIPEADREGVIRYVIGVGDAFRSEKSRQELNTIASKPPRDHVFQVNNFE
ALKTIQNQLREKGFAIEG

Ligands and cofactors

ID	Name	Formula	Copies
NI	Nickel (II) ion	Ni	2

Primary citation

Structural insight on the recognition of surface-bound opsonins by the integrin I domain of complement receptor 3. Bajic, G., Yatime, L., Sim, R.B. et al. Proc Natl Acad Sci U S A (2013) 110:16426-16431. DOI 10.1073/pnas.1311261110 · PubMed

Other PDB entries of the same protein (UniProt P01024 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2WY7 1.7 Å, Staphylococcus aureus complement subversion protein Sbi-IV in complex with complement…
2WY8 1.7 Å, Staphylococcus aureus complement subversion protein Sbi-IV in complex with complement…
7UE9 1.75 Å, Structure of anti-C3d Fab(3d8b) in complex with C3d
1C3D 1.8 Å, X-ray crystal structure of C3D: a C3 fragment and ligand for complement receptor 2
6RMT 2.0 Å, Crystal structure of disulphide-linked human C3d dimer
7BAG 2.0 Å, C3b in complex with CP40
1GHQ 2.04 Å, CR2-C3D complex structure
3D5R 2.1 Å, Crystal Structure of Efb-C (N138A) / C3d Complex
3OXU 2.1 Å, Complement components factor H CCP19-20 and C3d in complex
4I6O 2.14 Å, Crystal structure of chemically synthesized human anaphylatoxin C3a
4ONT 2.15 Å, Ternary host recognition complex of complement factor H, C3d, and sialic acid
2GOX 2.2 Å, Crystal structure of Efb-C / C3d Complex

Browse structure collections

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