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- PDB-2qos: Crystal structure of complement protein C8 in complex with a pept... -

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Basic information

Entry
Database: PDB / ID: 2qos
TitleCrystal structure of complement protein C8 in complex with a peptide containing the C8 binding site on C8
Components
  • Complement component 8, gamma polypeptide
  • Complement component C8 alpha chain
KeywordsIMMUNE SYSTEM / Beta barrel / lipocalin / Cleavage on pair of basic residues / Complement alternate pathway / Complement pathway / Cytolysis / EGF-like domain / Glycoprotein / Immune response / Innate immunity / Membrane attack complex / Polymorphism / Secreted
Function / homology
Function and homology information


Terminal pathway of complement / membrane attack complex / complement binding / complement activation / complement activation, alternative pathway / retinol binding / complement activation, classical pathway / Regulation of Complement cascade / positive regulation of immune response / blood microparticle ...Terminal pathway of complement / membrane attack complex / complement binding / complement activation / complement activation, alternative pathway / retinol binding / complement activation, classical pathway / Regulation of Complement cascade / positive regulation of immune response / blood microparticle / killing of cells of another organism / immune response / protein-containing complex binding / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
Complement component C8 gamma chain / : / Complement components C8A/B/C6, EGF-like domain / Membrane attack complex component/perforin/complement C9 / Alpha-1-microglobulin / Membrane attack complex component/perforin domain, conserved site / Membrane attack complex/perforin (MACPF) domain signature. / membrane-attack complex / perforin / MAC/Perforin domain / Membrane attack complex/perforin (MACPF) domain profile. ...Complement component C8 gamma chain / : / Complement components C8A/B/C6, EGF-like domain / Membrane attack complex component/perforin/complement C9 / Alpha-1-microglobulin / Membrane attack complex component/perforin domain, conserved site / Membrane attack complex/perforin (MACPF) domain signature. / membrane-attack complex / perforin / MAC/Perforin domain / Membrane attack complex/perforin (MACPF) domain profile. / Membrane attack complex component/perforin (MACPF) domain / Thrombospondin type 1 domain / Low-density lipoprotein receptor domain class A / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Lipocalin family conserved site / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Calycin beta-barrel core domain / Lipocalin/cytosolic fatty-acid binding domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 1. / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Complement component C8 alpha chain / Complement component C8 gamma chain / Complement component C8 gamma chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.81 Å
AuthorsLovelace, L.L. / Chiswell, B. / Slade, D.J. / Sodetz, J.M. / Lebioda, L.
CitationJournal: Mol.Immunol. / Year: 2008
Title: Crystal structure of complement protein C8gamma in complex with a peptide containing the C8gamma binding site on C8alpha: Implications for C8gamma ligand binding.
Authors: Lovelace, L.L. / Chiswell, B. / Slade, D.J. / Sodetz, J.M. / Lebioda, L.
History
DepositionJul 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Complement component 8, gamma polypeptide
A: Complement component C8 alpha chain


Theoretical massNumber of molelcules
Total (without water)20,5602
Polymers20,5602
Non-polymers00
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.942, 85.251, 41.899
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Complement component 8, gamma polypeptide


Mass: 19171.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C8G / Production host: Escherichia coli (E. coli) / References: UniProt: Q14CU0, UniProt: P07360*PLUS
#2: Protein/peptide Complement component C8 alpha chain / Complement component 8 subunit alpha


Mass: 1388.527 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence has been modified from the human / References: UniProt: P07357
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.63 Å3/Da / Density % sol: 53.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 26-28% PEG6K, 0.1M Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97531 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 19, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97531 Å / Relative weight: 1
ReflectionResolution: 1.81→50 Å / Num. all: 20571 / Num. obs: 19234 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 5.9 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.051 / Χ2: 1.678 / Net I/σ(I): 16.2
Reflection shellResolution: 1.81→1.87 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 5.2 / Num. unique all: 1454 / Χ2: 1.15 / % possible all: 73.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3data extraction
SERGUIControl Programdata collection
CNSphasing
RefinementStarting model: 2OVE

2ove


Resolution: 1.81→37.6 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 558 2.7 %random
Rwork0.204 ---
all-19053 --
obs-18729 91 %-
Solvent computationBsol: 64.701 Å2
Displacement parametersBiso mean: 26.107 Å2
Baniso -1Baniso -2Baniso -3
1-6.426 Å20 Å20 Å2
2---10.808 Å20 Å2
3---4.382 Å2
Refinement stepCycle: LAST / Resolution: 1.81→37.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1437 0 0 164 1601
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.168
X-RAY DIFFRACTIONc_mcbond_it2.1262.5
X-RAY DIFFRACTIONc_scbond_it3.1043
X-RAY DIFFRACTIONc_mcangle_it3.073
X-RAY DIFFRACTIONc_scangle_it4.6263.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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