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- PDB-3ojy: Crystal Structure of Human Complement Component C8 -

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Basic information

Entry
Database: PDB / ID: 3ojy
TitleCrystal Structure of Human Complement Component C8
Components
  • Complement component C8 alpha chain
  • Complement component C8 beta chain
  • Complement component C8 gamma chain
KeywordsIMMUNE SYSTEM / MACPf / lipocalin / COMPLEMENT
Function / homology
Function and homology information


Terminal pathway of complement / membrane attack complex / complement binding / complement activation, alternative pathway / complement activation / retinol binding / complement activation, classical pathway / Regulation of Complement cascade / extracellular vesicle / positive regulation of immune response ...Terminal pathway of complement / membrane attack complex / complement binding / complement activation, alternative pathway / complement activation / retinol binding / complement activation, classical pathway / Regulation of Complement cascade / extracellular vesicle / 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 / Membrane attack complex/perforin (MACPF) domain profile. / MAC/Perforin domain ...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 / Membrane attack complex/perforin (MACPF) domain profile. / MAC/Perforin domain / Membrane attack complex component/perforin (MACPF) domain / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Lipocalin family conserved site / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 1. / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
beta-D-mannopyranose / Complement component C8 alpha chain / Complement component C8 beta chain / Complement component C8 gamma chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsLovelace, L.L. / Cooper, C.L. / Sodetz, J.M. / Lebioda, L.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure of human C8 protein provides mechanistic insight into membrane pore formation by complement.
Authors: Lovelace, L.L. / Cooper, C.L. / Sodetz, J.M. / Lebioda, L.
History
DepositionAug 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 26, 2011Group: Database references
Revision 1.3Apr 16, 2014Group: Other
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 1.6Sep 6, 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

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Assembly

Deposited unit
A: Complement component C8 alpha chain
B: Complement component C8 beta chain
C: Complement component C8 gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,91713
Polymers143,3963
Non-polymers1,52110
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10110 Å2
ΔGint14 kcal/mol
Surface area56210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.575, 139.575, 127.160
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Complement component C8 alpha chain / Complement component 8 subunit alpha


Mass: 61782.992 Da / Num. of mol.: 1 / Fragment: unp residues 31-584 / Source method: isolated from a natural source / Details: plasma Cohn fraction III / Source: (natural) Homo sapiens (human) / Tissue: BLOOD / References: UniProt: P07357
#2: Protein Complement component C8 beta chain / Complement component 8 subunit beta


Mass: 61202.828 Da / Num. of mol.: 1 / Fragment: unp residues 55-591 / Source method: isolated from a natural source / Details: plasma Cohn fraction III / Source: (natural) Homo sapiens (human) / Tissue: BLOOD / References: UniProt: P07358
#3: Protein Complement component C8 gamma chain


Mass: 20410.105 Da / Num. of mol.: 1 / Fragment: unp residues 21-202 / Source method: isolated from a natural source / Details: plasma Cohn fraction III / Source: (natural) Homo sapiens (human) / Tissue: BLOOD / References: UniProt: P07360
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Sugar
ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 14-16% PEG 4K, 100mM TAPS pH 9.0, 400mM NaCl, 10mM SrCl2, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR / Detector: CCD / Date: Jul 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 44803 / % possible obs: 93.3 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.101 / Χ2: 1.929 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.541.80.41715471.042163.7
2.54-2.591.90.41816321.134168.8
2.59-2.641.90.41817781.569174.8
2.64-2.6920.42419981.303183.7
2.69-2.752.10.42421591.23190
2.75-2.822.40.42422841.41196
2.82-2.892.70.42323671.405198.5
2.89-2.963.10.44523671.758199.2
2.96-3.053.50.38723571.504199.3
3.05-3.153.70.32823871.465199.3
3.15-3.263.80.26623691.517199
3.26-3.393.90.2123871.629199.5
3.39-3.553.90.15423921.869199.2
3.55-3.733.80.12123522.093199.3
3.73-3.973.80.10223992.294199.5
3.97-4.273.80.0823912.428199.5
4.27-4.73.80.06523902.702199.4
4.7-5.383.70.05724092.533199.5
5.38-6.783.70.05124082.275199.5
6.78-503.70.03424302.366198.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
SERGUISerguidata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2RD7

2rd7


Resolution: 2.51→45.69 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.835 / WRfactor Rfree: 0.3204 / WRfactor Rwork: 0.2353 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.7231 / SU B: 14.368 / SU ML: 0.324 / SU R Cruickshank DPI: 0.839 / SU Rfree: 0.4114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.411 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3374 2267 5.1 %RANDOM
Rwork0.2488 ---
obs0.2532 44756 93.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.61 Å2 / Biso mean: 52.0136 Å2 / Biso min: 17.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20.35 Å20 Å2
2--0.69 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 2.51→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9144 0 90 0 9234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0219461
X-RAY DIFFRACTIONr_angle_refined_deg1.7741.97412799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2651134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.72723.697468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.69151583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6981576
X-RAY DIFFRACTIONr_chiral_restr0.1320.21354
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217222
X-RAY DIFFRACTIONr_mcbond_it0.821.55676
X-RAY DIFFRACTIONr_mcangle_it1.56529099
X-RAY DIFFRACTIONr_scbond_it2.01633785
X-RAY DIFFRACTIONr_scangle_it3.3364.53700
LS refinement shellResolution: 2.51→2.575 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.453 103 -
Rwork0.309 2137 -
all-2240 -
obs--63.21 %

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