› 5fob

X-ray diffraction
2.6Å resolution

Crystal Structure of Human Complement C3b in complex with Smallpox Inhibitor of Complement (SPICE)

Released:
DOI: 10.2210/pdb5fob/pdb
PDB entry 5fob coloured by chain, front view.
PDB entry 5fob coloured by chain, side view.
PDB entry 5fob coloured by chain, top view.
Source organisms:
Primary publication:
Regulators of complement activity mediate inhibitory mechanisms through a common C3b-binding mode.
Forneris F, Wu J, Xue X, Ricklin D, Lin Z, Sfyroera G, Tzekou A, Volokhina E, Granneman JC, Hauhart R, Bertram P, Liszewski MK, Atkinson JP, Lambris JD, Gros P
EMBO J 35 1133-49 (2016)
PMID: 27013439

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133833 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (5 distinct):
Complement C3 beta chain Chain: A
Molecule details ›
Chain: A
Length: 645 amino acids
Theoretical weight: 71.39 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P01024 (Residues: 23-667; Coverage: 39%)
Gene names: C3, CPAMD1
Sequence domains:
Structure domains:
Complement C3b alpha' chain Chain: B
Molecule details ›
Chain: B
Length: 915 amino acids
Theoretical weight: 104.07 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P01024 (Residues: 749-1663; Coverage: 56%)
Gene names: C3, CPAMD1
Sequence domains:
Structure domains:
Sushi domain-containing protein Chain: C
Molecule details ›
Chain: C
Length: 245 amino acids
Theoretical weight: 26.87 KDa
Source organism: Variola major virus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q76U65 (Residues: 19-263; Coverage: 93%)
Gene names: 13-62_L1, 6-58_L1, Aziz_L1, D15L, Helder_L1, Ind-3a_L1, Ind-4a_L1, Khateen_L1, Kuw-5_L1, M-A-60_L1, M-Abr-60_L1, M-Bl-60_L1, M-Gavr-60_L1, M-N-60_L1, M-Sur-60_L1, Mary_L1, Ngami_L1, Rw-18_L1, VARV_AFG70_vlt4_015, VARV_BEN68_59_015, VARV_BOT72_143_015, VARV_BOT73_225_015, VARV_BSH74_nur_015, VARV_BSH74_shz_015, VARV_BSH74_sol_015, VARV_BSH75_banu_015, VARV_CHN48_horn_015, VARV_ETH72_16_015, VARV_ETH72_17_015, VARV_GER58_hdlg_015, VARV_GUI69_005_015, VARV_IND53_mad_015, VARV_IND53_ndel_015, VARV_IND64_vel4_015, VARV_IND64_vel5_015, VARV_IRN72_tbrz_015, VARV_JAP51_hrpr_015, VARV_JAP51_stwl_015, VARV_KOR47_lee_015, VARV_KUW67_1629_015, VARV_NEP73_175_015, VARV_NIG69_001_015, VARV_PAK69_lah_015, VARV_SAF65_102_015, VARV_SAF65_103_015, VARV_SLN68_258_015, VARV_SOM77_1252_015, VARV_SOM77_1605_015, VARV_SOM77_ali_015, VARV_SUD47_jub_015, VARV_SUD47_rum_015, VARV_SUM70_222_015, VARV_SUM70_228_015, VARV_SYR72_119_015, VARV_TAN65_kem_015, VARV_UNK44_harv_015, VARV_UNK46_hind_015, VARV_UNK47_hig_015, VARV_YUG72_164_015, Wzim_Ahmed_L1
Sequence domains: Sushi repeat (SCR repeat)

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
4 bound ligands:
Ligand CL 5 x CL
Ligand GOL 24 x GOL
Ligand NA 2 x NA
Ligand IOD 7 x IOD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: P1
Unit cell:
a: 68.891Å b: 83.311Å c: 127.377Å
α: 75.03° β: 76.2° γ: 68.5°
R-values:
R R work R free
0.199 0.198 0.23
Expression system: Escherichia coli

Quick links

Citations

21 review citations

Novel mechanisms and functions of complement.
Hajishengallis et al. (2017)
20 more

4 mentions without citation

Complement component C3: A structural perspective and potential therapeutic implications.
Geisbrecht et al. (2022)
3 more