3OED: Complement C3

The structure of the complex between complement receptor CR2 and its ligand complement fragment C3d. Determined by X-ray diffraction at 3.16 Å resolution. Released 11 May 2011.

Method: X-ray diffraction
Resolution: 3.16 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,628
Mol. weight: 99.15 kDa
Released: 11 May 2011

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

Secondary structure: helices and β-sheets

3OED contains 38 α-helices and 53 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: 16 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	4-10	7
α-helix	20-37	18
α-helix	48-64	17
β-strand	67	1	1
β-strand	73	1	1
α-helix	80-82	3
α-helix	83-96	14
β-strand	100	1	2
β-strand	102-103	2	3
α-helix	104-118	15
β-strand	119	1	4
α-helix	124	1
β-strand	125	1	4
α-helix	126-127	2
α-helix	138-141	4
α-helix	146-165	20
α-helix	172-187	16
α-helix	193-205	13
α-helix	211-220	10
α-helix	233-250	18
α-helix	257-264	8
α-helix	275-292	18

Chain B: 16 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
α-helix	8-10	3
α-helix	20-37	18
α-helix	41-44	4
α-helix	47-64	18
β-strand	67	1	13
β-strand	73	1	13
α-helix	80-81	2
α-helix	83-96	14
β-strand	100	1	14
β-strand	102-103	2	15
α-helix	104-118	15
β-strand	119	1	16
β-strand	125	1	16
α-helix	134-141	8
α-helix	146-165	20
α-helix	172-187	16
α-helix	193-205	13
α-helix	212-218	7
β-strand	222	1	17
β-strand	226	1	17
α-helix	233-250	18
α-helix	256-265	10
α-helix	276-292	17

Chain C: 3 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	5
β-strand	12-14	3	6
β-strand	16	1	2
β-strand	21-22	2	5
β-strand	25-28	4	3
β-strand	29-31	3	6
β-strand	35-38	4	7
β-strand	42-44	3	3
β-strand	45-46	2	8
β-strand	54-55	2	8
α-helix	58-60	3
β-strand	61-64	4	7
β-strand	70	1	9
α-helix	72-74	3
β-strand	79-81	3	10
β-strand	89	1	9
β-strand	93-95	3	11
β-strand	96-98	3	10
β-strand	103-105	3	12
β-strand	109-112	4	11
β-strand	118-119	2	11
α-helix	122-124	3
β-strand	125-127	3	12

Chain D: 3 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	18
α-helix	5-7	3
β-strand	12-14	3	19
β-strand	16	1	14
β-strand	21-22	2	18
β-strand	25-28	4	15
β-strand	29-31	3	19
β-strand	35-38	4	20
β-strand	42-44	3	15
β-strand	45-46	2	21
β-strand	54-55	2	21
α-helix	58-60	3
β-strand	61-64	4	20
β-strand	79-81	3	22
β-strand	95	1	23
β-strand	96-98	3	22
β-strand	102-105	4	24
β-strand	109	1	23
β-strand	111-112	2	25
β-strand	118-119	2	25
α-helix	122-124	3
β-strand	125-128	4	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Complement C3	A, B	protein	310	Homo sapiens	P01024 (AlphaFold model)
Complement receptor type 2	C, D	protein	135	Homo sapiens	P20023 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3OED_1 Complement C3 (chains A, B)
MLDAERLKHLIVTPSGAGEQNMIGMTPTVIAVHYLDETEQWEKFGLEKRQGALELIKKGY
TQQLAFRQPSSAFAAFVKRAPSTWLTAYVVKVFSLAVNLIAIDSQVLCGAVKWLILEKQK
PDGVFQEDAPVIHQEMIGGLRNNNEKDMALTAFVLISLQEAKDICEEQVNSLPGSITKAG
DFLEANYMNLQRSYTVAIAGYALAQMGRLKGPLLNKFLTTAKDKNRWEDPGKQLYNVEAT
SYALLALLQLKDFDFVPPVVRWLNEQRYYGGGYGSTQATFMVFQALAQYQKDAPDHQELN
LDVSLQLPSR

Sequence of entity 2 (C, D), FASTA

>3OED_2 Complement receptor type 2 (chains C, D)
MGISCGSPPPILNGRISYYSTPIAVGTVIRYSCSGTFRLIGEKSLLCITKDKVDGTWDKP
APKCEYFNKYSSCPEPIVPGGYKIRGSTPYRHGDSVTFACKTNFSMNGNKSVWCQANNMW
GPTRLPTCVSVFPLE

Primary citation

A crystal structure of the complex between human complement receptor 2 and its ligand C3d. van den Elsen, J.M., Isenman, D.E. Science (2011) 332:608-611. DOI 10.1126/science.1201954 · 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

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