6RMT: Disulphide-linked human C3d dimer

Crystal structure of disulphide-linked human C3d dimer. Determined by X-ray diffraction at 2.0 Å resolution. Released 18 Nov 2020.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,401
Mol. weight: 69.7 kDa
Released: 18 Nov 2020

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

Secondary structure: helices and β-sheets

6RMT contains 38 α-helices and 12 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: 19 helices, 6 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	48-63	16
α-helix	64-66	3
β-strand	67	1	1
β-strand	73	1	1
α-helix	80-82	3
α-helix	83-96	14
α-helix	104-113	10
α-helix	114-118	5
β-strand	119	1	2
β-strand	125	1	2
α-helix	134-140	7
α-helix	146-165	20
α-helix	172-186	15
α-helix	187-189	3
α-helix	193-205	13
α-helix	211-220	10
β-strand	222	1	3
β-strand	226	1	3
α-helix	233-250	18
α-helix	256-265	10
α-helix	276-292	17

Chain B: 19 helices, 6 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	48-64	17
β-strand	67	1	4
β-strand	73	1	4
α-helix	80-82	3
α-helix	83-95	13
α-helix	96-98	3
α-helix	104-113	10
α-helix	114-118	5
β-strand	119	1	5
β-strand	125	1	5
α-helix	134-141	8
α-helix	146-165	20
α-helix	172-186	15
α-helix	187-189	3
α-helix	193-205	13
α-helix	211-219	9
β-strand	222	1	6
β-strand	226	1	6
α-helix	233-249	17
α-helix	256-265	10
α-helix	276-292	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Complement C3	A, B	protein	310	Homo sapiens	P01024 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6RMT_1 Complement C3 (chains A, B)
MLDAERLKHLIVTPSGCGEQNMIGMTPTVIAVHYLDETEQWEKFGLEKRQGALELIKKGY
TQQLAFRQPSSAFAAFVKRAPSTWLTAYVVKVFSLAVNLIAIDSQVLCGAVKWLILEKQK
PDGVFQEDAPVIHQEMIGGLRNNNEKDMALTAFVLISLQEAKDICEEQVNSLPGSITKAG
DFLEANYMNLQRSYTVAIAGYALAQMGRLKGPLLNKFLTTAKDKNRWEDPGKQLYNVEAT
SYALLALLQLKDFDFVPPVVRWLNEQRYYGGGYGSTQATFMVFQALAQYQKDAPDHQELN
LDVSLQLPSR

Primary citation

Insights Into the Structure-Function Relationships of Dimeric C3d Fragments. Wahid, A.A., Dunphy, R.W., Macpherson, A. et al. Front Immunol (2021) 12:714055-714055. DOI 10.3389/fimmu.2021.714055 · 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
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
4ZH1 2.24 Å, Complement factor H in complex with the GM1 glycan

Browse structure collections

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