3D5R: Efb-C (N138A) / C3d Complex

Crystal Structure of Efb-C (N138A) / C3d Complex. Determined by X-ray diffraction at 2.1 Å resolution. Released 9 Sept 2008.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Homo sapiens, Staphylococcus aureus subsp. aureus str. Newman
Chains: 4
Atoms: 5,868
Mol. weight: 81.39 kDa
Released: 9 Sept 2008

Explore 3D5R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3D5R contains 44 α-helices and 12 β-strands across 4 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: 17 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
α-helix	8-14	7
α-helix	24-41	18
α-helix	50-68	19
β-strand	71	1	1
β-strand	77	1	1
α-helix	84-86	3
α-helix	87-99	13
α-helix	100-102	3
α-helix	108-122	15
β-strand	123	1	2
β-strand	129	1	2
α-helix	138-145	8
α-helix	150-169	20
α-helix	170-172	3
α-helix	176-191	16
α-helix	197-209	13
α-helix	215-224	10
β-strand	226	1	3
β-strand	230	1	3
α-helix	237-254	18
α-helix	260-270	11
α-helix	280-296	17

Chain B: 19 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5
α-helix	8-14	7
α-helix	24-41	18
α-helix	50-68	19
β-strand	71	1	4
β-strand	77	1	4
α-helix	84-86	3
α-helix	87-99	13
α-helix	100-102	3
α-helix	108-117	10
α-helix	118-122	5
β-strand	123	1	5
β-strand	129	1	5
α-helix	138-145	8
α-helix	150-169	20
α-helix	170-172	3
α-helix	176-190	15
α-helix	191-193	3
α-helix	197-209	13
α-helix	215-224	10
β-strand	226	1	6
β-strand	230	1	6
α-helix	237-254	18
α-helix	260-270	11
α-helix	280-296	17

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	12-34	23
α-helix	37-48	12
α-helix	52-54	3
α-helix	55-71	17

Chain D: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	12-34	23
α-helix	37-49	13
α-helix	52-54	3
α-helix	55-71	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Complement C3	A, B	protein	297	Homo sapiens	P01024 (AlphaFold model)
Fibrinogen-binding protein	C, D	protein	65	Staphylococcus aureus subsp. aureus str. Newman	A6QG59 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3D5R_1 Complement C3 (chains A, B)
GSRSTDAERLKHLIVTPSGAGEQNMIGMTPTVIAVHYLDETEQWEKFGLEKRQGALELIK
KGYTQQLAFRQPSSAFAAFVKRAPSTWLTAYVVKVFSLAVNLIAIDSQVLCGAVKWLILE
KQKPDGVFQEDAPVIHQEMIGGLRNNNEKDMALTAFVLISLQEAKDICEEQVNSLPGSIT
KAGDFLEANYMNLQRSYTVAIAGYALAQMGRLKGPLLNKFLTTAKDKNRWEDPGKQLYNV
EATSYALLALLQLKDFDFVPPVVRWLNEQRYYGGGYGSTQATFMVFQALAQYQKDAP

Sequence of entity 2 (C, D), FASTA

>3D5R_2 Fibrinogen-binding protein (chains C, D)
TDATIKKEQKLIQAQNLVREFEKTHTVSAHRKAQKAVALVSFEYKVKKMVLQERIDNVLK
QGLVR

Primary citation

Electrostatic contributions drive the interaction between Staphylococcus aureus protein Efb-C and its complement target C3d. Haspel, N., Ricklin, D., Geisbrecht, B.V. et al. Protein Sci (2008) 17:1894-1906. DOI 10.1110/ps.036624.108 · 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
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
4ZH1 2.24 Å, Complement factor H in complex with the GM1 glycan

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