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- PDB-2qki: Human C3c in complex with the inhibitor compstatin -

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Basic information

Entry
Database: PDB / ID: 2qki
TitleHuman C3c in complex with the inhibitor compstatin
Components
  • (Complement C3Complement component 3) x 3
  • compstatin
KeywordsImmune system/hydrolase inhibitor / immunity / complement inhibitor design / C3 / compstatin / Immune system-hydrolase inhibitor complex
Function / homology
Function and homology information


oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway ...oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of phagocytosis, engulfment / complement receptor mediated signaling pathway / Activation of C3 and C5 / positive regulation of type IIa hypersensitivity / positive regulation of glucose transmembrane transport / complement-dependent cytotoxicity / complement activation, alternative pathway / complement activation / neuron remodeling / endopeptidase inhibitor activity / amyloid-beta clearance / positive regulation of vascular endothelial growth factor production / Purinergic signaling in leishmaniasis infection / complement activation, classical pathway / Peptide ligand-binding receptors / fatty acid metabolic process / Regulation of Complement cascade / Post-translational protein phosphorylation / response to bacterium / positive regulation of receptor-mediated endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of angiogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / G alpha (i) signalling events / blood microparticle / secretory granule lumen / immune response / inflammatory response / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
N-terminal domain of TfIIb - #160 / S-adenosyl-L-methionine-dependent methyltransferases - #20 / Immunoglobulin-like - #1940 / Alpha-macroglobulin, receptor-binding domain / Macroglobulin (MG2) domain / S-adenosyl-L-methionine-dependent methyltransferases / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / N-terminal domain of TfIIb / : / : ...N-terminal domain of TfIIb - #160 / S-adenosyl-L-methionine-dependent methyltransferases - #20 / Immunoglobulin-like - #1940 / Alpha-macroglobulin, receptor-binding domain / Macroglobulin (MG2) domain / S-adenosyl-L-methionine-dependent methyltransferases / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / N-terminal domain of TfIIb / : / : / Complement component 3, CUB domain 2 / Complement component 3, CUB domain 1 / Complement C3-like, NTR domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / : / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin/fibulin / Anaphylatoxin, complement system / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Netrin domain / NTR domain profile. / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor binding domain / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Other non-globular / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Single Sheet / Special / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
BROMIDE ION / : / Complement C3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsJanssen, B.J.C. / Halff, E.F. / Lambris, J.D. / Gros, P.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structure of compstatin in complex with complement component C3c reveals a new mechanism of complement inhibition.
Authors: Janssen, B.J. / Halff, E.F. / Lambris, J.D. / Gros, P.
History
DepositionJul 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement C3
B: Complement C3
C: Complement C3
D: Complement C3
E: Complement C3
F: Complement C3
G: compstatin
H: compstatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)273,11365
Polymers267,8548
Non-polymers5,25957
Water8,485471
1
A: Complement C3
B: Complement C3
C: Complement C3
G: compstatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,03326
Polymers133,9274
Non-polymers2,10622
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Complement C3
E: Complement C3
F: Complement C3
H: compstatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,08039
Polymers133,9274
Non-polymers3,15335
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.809, 124.754, 127.367
Angle α, β, γ (deg.)90.00, 95.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 6 molecules ADBECF

#1: Protein Complement C3 / Complement component 3


Mass: 71267.203 Da / Num. of mol.: 2 / Fragment: residues 23-665 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024
#2: Protein Complement C3 / Complement component 3


Mass: 21521.756 Da / Num. of mol.: 2 / Fragment: residues 749-936 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024
#3: Protein Complement C3 / Complement component 3


Mass: 39537.418 Da / Num. of mol.: 2 / Fragment: residues 1321-1663 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024

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Protein/peptide / Sugars , 2 types, 4 molecules GH

#4: Protein/peptide compstatin


Mass: 1600.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic peptide
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 526 molecules

#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#7: Chemical...
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Br
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAuthors state residue 292 is a polymorphic site, which can be either Proline or Leucine.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG-MME 2000, KBr, Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 14, 2005
RadiationMonochromator: Single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.4→33 Å / Num. all: 104399 / Num. obs: 100641 / % possible obs: 96.4 % / Observed criterion σ(F): -999 / Observed criterion σ(I): -3.7 / Redundancy: 3 % / Biso Wilson estimate: 49.9 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.4
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 2.4 / Num. unique all: 14898 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.3.0008refinement
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2A74

2a74


Resolution: 2.4→33 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.887 / SU B: 19.512 / SU ML: 0.241 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.488 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28093 5005 5 %RANDOM
Rwork0.21302 ---
all0.216 95439 --
obs0.216 95439 96.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.14 Å2
Baniso -1Baniso -2Baniso -3
1-4.09 Å20 Å2-1.15 Å2
2---2.76 Å20 Å2
3----1.53 Å2
Refinement stepCycle: LAST / Resolution: 2.4→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17808 0 201 471 18480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02218341
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.97424859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.18752229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.76424.785813
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.176153227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1011595
X-RAY DIFFRACTIONr_chiral_restr0.0910.22830
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213573
X-RAY DIFFRACTIONr_nbd_refined0.2010.27552
X-RAY DIFFRACTIONr_nbtor_refined0.3020.212099
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2819
X-RAY DIFFRACTIONr_metal_ion_refined0.1220.211
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.2141
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.213
X-RAY DIFFRACTIONr_mcbond_it0.441.511207
X-RAY DIFFRACTIONr_mcangle_it0.834218285
X-RAY DIFFRACTIONr_scbond_it1.21637214
X-RAY DIFFRACTIONr_scangle_it2.0294.56566
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 380 -
Rwork0.262 7127 -
obs--98.09 %

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