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- PDB-4a5w: Crystal structure of C5b6 -

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Basic information

Entry
Database: PDB / ID: 4a5w
TitleCrystal structure of C5b6
Components
  • COMPLEMENT C5Complement component 5
  • COMPLEMENT COMPONENT C6
KeywordsIMMUNE SYSTEM / IMMUNITY / MEMBRANE ATTACK COMPLEX
Function / homology
Function and homology information


Terminal pathway of complement / membrane attack complex / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / complement activation / chemokine activity / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway ...Terminal pathway of complement / membrane attack complex / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / complement activation / chemokine activity / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / positive regulation of chemokine production / Peptide ligand-binding receptors / Regulation of Complement cascade / chemotaxis / positive regulation of immune response / G alpha (i) signalling events / killing of cells of another organism / in utero embryonic development / cell surface receptor signaling pathway / inflammatory response / G protein-coupled receptor signaling pathway / signaling receptor binding / innate immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
TSP-1 type 1 repeat / Thrombospondin type-1 (TSP1) repeat / : / Complement component C6, KAZAL domain / : / Complement components C8A/B/C6, EGF-like domain / Membrane attack complex component/perforin/complement C9 / Factor I / membrane attack complex / factor I membrane attack complex / Membrane attack complex component/perforin domain, conserved site ...TSP-1 type 1 repeat / Thrombospondin type-1 (TSP1) repeat / : / Complement component C6, KAZAL domain / : / Complement components C8A/B/C6, EGF-like domain / Membrane attack complex component/perforin/complement C9 / Factor I / membrane attack complex / factor I membrane attack complex / Membrane attack complex component/perforin domain, conserved site / Membrane attack complex/perforin (MACPF) domain signature. / : / Complement component 5, CUB domain / membrane-attack complex / perforin / Membrane attack complex/perforin (MACPF) domain profile. / MAC/Perforin domain / Membrane attack complex component/perforin (MACPF) domain / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Complement Module, domain 1 / 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 / Complement Module; domain 1 / Kazal domain / Kazal domain profile. / 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 / 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 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/SCR/CCP superfamily / Sushi/CCP/SCR domain profile. / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Single Sheet / EGF-like domain signature 1. / Ribbon / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
beta-D-mannopyranose / alpha-L-fucopyranose / Complement C5 / Complement component C6
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsHadders, M.A. / Bubeck, D. / Forneris, F. / Pangburn, M. / Llorca, O. / Lea, S.M. / Gros, P.
CitationJournal: Cell Rep / Year: 2012
Title: Assembly and regulation of the membrane attack complex based on structures of C5b6 and sC5b9.
Authors: Michael A Hadders / Doryen Bubeck / Pietro Roversi / Svetlana Hakobyan / Federico Forneris / B Paul Morgan / Michael K Pangburn / Oscar Llorca / Susan M Lea / Piet Gros /
Abstract: Activation of the complement system results in formation of membrane attack complexes (MACs), pores that disrupt lipid bilayers and lyse bacteria and other pathogens. Here, we present the crystal ...Activation of the complement system results in formation of membrane attack complexes (MACs), pores that disrupt lipid bilayers and lyse bacteria and other pathogens. Here, we present the crystal structure of the first assembly intermediate, C5b6, together with a cryo-electron microscopy reconstruction of a soluble, regulated form of the pore, sC5b9. Cleavage of C5 to C5b results in marked conformational changes, distinct from those observed in the homologous C3-to-C3b transition. C6 captures this conformation, which is preserved in the larger sC5b9 assembly. Together with antibody labeling, these structures reveal that complement components associate through sideways alignment of the central MAC-perforin (MACPF) domains, resulting in a C5b6-C7-C8β-C8α-C9 arc. Soluble regulatory proteins below the arc indicate a potential dual mechanism in protection from pore formation. These results provide a structural framework for understanding MAC pore formation and regulation, processes important for fighting infections and preventing complement-mediated tissue damage.
History
DepositionOct 28, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Other
Revision 1.2Oct 31, 2012Group: Database references
Revision 1.3Nov 13, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp / pdbx_database_related ...chem_comp / pdbx_database_related / pdbx_database_status / struct_conn
Item: _chem_comp.type / _pdbx_database_related.content_type ..._chem_comp.type / _pdbx_database_related.content_type / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_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 1.5Dec 20, 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 C5
B: COMPLEMENT COMPONENT C6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,87811
Polymers280,2492
Non-polymers1,6309
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8290 Å2
ΔGint-1.9 kcal/mol
Surface area127550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.217, 230.747, 269.983
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein COMPLEMENT C5 / Complement component 5 / C3 AND PZP-LIKE ALPHA-2-MACROGLOBULIN DOMAIN-CONTAINING PROTEIN 4 / COMPLEMENT C5 BETA CHAIN / ...C3 AND PZP-LIKE ALPHA-2-MACROGLOBULIN DOMAIN-CONTAINING PROTEIN 4 / COMPLEMENT C5 BETA CHAIN / COMPLEMENT C5 ALPHA CHAIN / C5A ANAPHYLATOXIN / COMPLEMENT C5 ALPHA' CHAIN / C5B


Mass: 177707.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Tissue: BLOOD / References: UniProt: P01031
#2: Protein COMPLEMENT COMPONENT C6


Mass: 102541.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Tissue: BLOOD / References: UniProt: P13671

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Sugars , 3 types, 8 molecules

#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose / Fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: 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.: 3
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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Non-polymers , 1 types, 1 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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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: 4.25 Å3/Da / Density % sol: 71 % / Description: NONE
Crystal growpH: 7.8 / Details: 167 MM HEPES-NAOH PH7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97623
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 59023 / % possible obs: 95.8 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 98.41 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.4
Reflection shellResolution: 3.9→4 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 1.7 / % possible all: 97.1

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3CU7, 3OJY, 2OK5

3cu7

3ojy

2ok5


Resolution: 3.5→46.19 Å / Cor.coef. Fo:Fc: 0.8931 / Cor.coef. Fo:Fc free: 0.8864 / Cross valid method: THROUGHOUT / σ(F): 0
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=NAG CA FUC BMA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=18928. NUMBER WITH APPROX DEFAULT CCP4 ATOM ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=NAG CA FUC BMA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=18928. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=99. NUMBER TREATED BY BAD NON- BONDED CONTACTS=1.
RfactorNum. reflection% reflectionSelection details
Rfree0.2697 1214 2.06 %RANDOM
Rwork0.2555 ---
obs0.2558 59017 --
Displacement parametersBiso mean: 157.24 Å2
Baniso -1Baniso -2Baniso -3
1--8.837 Å20 Å20 Å2
2--0.1298 Å20 Å2
3---8.7072 Å2
Refine analyzeLuzzati coordinate error obs: 1.207 Å
Refinement stepCycle: LAST / Resolution: 3.5→46.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18928 0 100 0 19028
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00719482HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0426326HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6788SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes518HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2781HARMONIC5
X-RAY DIFFRACTIONt_it19479HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.7
X-RAY DIFFRACTIONt_other_torsion18.1
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2587SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact22866SEMIHARMONIC4
LS refinement shellResolution: 3.5→3.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2248 91 2.25 %
Rwork0.2292 3950 -
all0.2291 4041 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.6383-1.707-2.66734.5854-0.54381.42230.0286-0.04220.02240.12990.0936-0.30290.07430.4027-0.12210.00540.1278-0.04350.2619-0.1206-0.074243.9731-20.2155-33.5936
21.66560.00650.2920.9620.61130.54860.1858-0.05170.13830.157-0.11160.08910.0380.1046-0.07430.29810.05990.00830.1192-0.0078-0.04866.537-11.7245-25.7475
32.1729-0.7135-0.27191.32730.15531.17750.0944-0.4127-0.38660.51560.00970.07410.52740.3345-0.10410.4349-0.0072-0.14820.1066-0.0355-0.327415.5645-27.9654-11.9654
41.63980.0784-0.37170.90620.2932.00960.22720.47830.0997-0.0366-0.0576-0.0733-0.08870.0636-0.1696-0.0890.21490.004-0.12410.0929-0.34610.2338-11.9509-52.9164
54.6907-1.0969-2.15782.08192.59485.65950.03640.3940.3316-0.01720.2352-0.2041-0.13990.6574-0.2717-0.040.20620.00720.1210.0333-0.30194.4325-14.2791-59.1429
62.6849-3.446-0.28273.81310.51930.007-0.02660.44840.1180.070.2195-0.1831-0.1381-0.1283-0.19290.1575-0.09390.23260.24150.1935-0.1035-45.01581.581-23.948
70-1.3833-0.46784.4683-0.27760.26630.0250.02690.07380.1837-0.16730.28450.1770.16620.14230.07320.32290.33370.12930.16110.134684.2495-53.8429-102.2
81.74010.2599-0.84941.5019-0.20771.61420.1649-0.3195-0.23210.4201-0.1187-0.45720.59970.0093-0.04620.10020.08770.0223-0.0234-0.0823-0.01841.3752-58.3017-50.9697
91.21870.0228-0.6332.234-0.19991.2089-0.2322-0.1451-0.1729-0.24490.0082-0.49990.3998-0.14810.2240.23080.17690.2342-0.1125-0.04680.030846.5724-60.5097-66.5556
102.52120.5552.91971.97480.66593.0125-0.01610.5601-0.1772-0.09550.03660.71090.3185-0.1877-0.02050.03560.019-0.26220.2577-0.2091-0.0904-15.2354-25.6086-69.183
115.47681.0606-0.29790.03310.59653.19280.02340.1916-0.03740.03660.3627-0.345-0.12460.1213-0.3860.13720.2523-0.1437-0.24270.0770.094-43.2402-49.1216-110.47
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESSEQ 22 : 112
2X-RAY DIFFRACTION2CHAIN A AND RESSEQ 113 : 253
3X-RAY DIFFRACTION3CHAIN A AND RESSEQ 254 : 772
4X-RAY DIFFRACTION4CHAIN A AND RESSEQ 773 : 1234
5X-RAY DIFFRACTION5CHAIN A AND RESSEQ 1243 : 1375
6X-RAY DIFFRACTION6CHAIN A AND RESSEQ 1376 : 1676
7X-RAY DIFFRACTION7CHAIN B AND RESSEQ 22 : 79
8X-RAY DIFFRACTION8CHAIN B AND RESSEQ 80 : 304
9X-RAY DIFFRACTION9CHAIN B AND RESSEQ 305 : 642
10X-RAY DIFFRACTION10CHAIN B AND RESSEQ 643 : 767
11X-RAY DIFFRACTION11CHAIN B AND RESSEQ 768 : 934

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