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- PDB-3t5o: Crystal Structure of human Complement Component C6 -

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Basic information

Entry
Database: PDB / ID: 3t5o
TitleCrystal Structure of human Complement Component C6
ComponentsComplement component C6
KeywordsIMMUNE SYSTEM / MACPF / MAC / MEMBRANE ATTACK COMPLEX / COMPLEMENT / INNATE IMMUNE SYSTEM / BLOOD / MEMBRANE / C7 / C8 / C9 / CYTOLYSIN
Function / homology
Function and homology information


Terminal pathway of complement / membrane attack complex / complement activation / complement activation, classical pathway / Regulation of Complement cascade / positive regulation of immune response / killing of cells of another organism / in utero embryonic development / innate immune response / extracellular space ...Terminal pathway of complement / membrane attack complex / complement activation / complement activation, classical pathway / Regulation of Complement cascade / positive regulation of immune response / killing of cells of another organism / in utero embryonic development / 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. / membrane-attack complex / perforin / Membrane attack complex/perforin (MACPF) domain profile. / MAC/Perforin domain / Membrane attack complex component/perforin (MACPF) domain / Complement Module, domain 1 / Complement Module; domain 1 / Kazal domain / Kazal domain profile. / 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. / Single Sheet / EGF-like domain signature 1. / Ribbon / Mainly Beta
Similarity search - Domain/homology
: / beta-L-fucopyranose / alpha-D-mannopyranose / Complement component C6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.869 Å
AuthorsAleshin, A.E. / Stec, B. / Bankston, L.A. / DiScipio, R.G. / Liddington, R.C.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structure of Complement C6 Suggests a Mechanism for Initiation and Unidirectional, Sequential Assembly of Membrane Attack Complex (MAC).
Authors: Aleshin, A.E. / Schraufstatter, I.U. / Stec, B. / Bankston, L.A. / Liddington, R.C. / Discipio, R.G.
History
DepositionJul 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2012Group: Database references
Revision 1.2Apr 11, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / 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_close_contact / 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.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_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_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_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement component C6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,2899
Polymers102,5411
Non-polymers1,7488
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.810, 180.150, 60.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein / Non-polymers , 2 types, 2 molecules A

#1: Protein Complement component C6


Mass: 102541.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P13671
#4: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd

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Sugars , 4 types, 7 molecules

#2: 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.: 1
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
#3: Polysaccharide beta-D-glucopyranose-(1-3)-alpha-L-fucopyranose


Type: oligosaccharide / Mass: 326.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3LFucpa1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1221m-1a_1-5][a2122h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-L-Fucp]{[(3+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-FUL / beta-L-fucopyranose / 6-DEOXY-BETA-L-GALACTOSE / Fucose


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-fucopyranoseCOMMON NAMEGMML 1.0
b-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Sugar
ChemComp-MAN / alpha-D-mannopyranose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-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: 3.9 Å3/Da / Density % sol: 68.49 %
Crystal growTemperature: 284 K / pH: 5.8
Details: 5 mM MES, 89 mM Sodium Chloride, 0.01 mM Cadmium Chloride, pH 5.8, EVAPORATION, temperature 284K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.991
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 4, 2009 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.991 Å / Relative weight: 1
ReflectionResolution: 2.86→49 Å / Num. obs: 35745 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 6.4
Reflection shellResolution: 2.86→3.04 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.5 / % possible all: 60.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SHARPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.869→43.057 Å / SU ML: 0.42 / σ(F): 1.34 / Phase error: 27.34 / Stereochemistry target values: ML
Details: THE LAST DOMAIN (RESIDUES 834-913) WAS BUILT BY THREADING THE AMINO ACID SEQUENCE ON THE NMR STRUCTURE OF SAME DOMAIN FROM C7 (PDB ENTRY 2WCY). SINCE THE ELECTRON DENSITY WAS WEAK, THE ...Details: THE LAST DOMAIN (RESIDUES 834-913) WAS BUILT BY THREADING THE AMINO ACID SEQUENCE ON THE NMR STRUCTURE OF SAME DOMAIN FROM C7 (PDB ENTRY 2WCY). SINCE THE ELECTRON DENSITY WAS WEAK, THE SEQUENCE ANNOTATION IS NOT RELIABLE.
RfactorNum. reflection% reflection
Rfree0.2759 2179 6.1 %
Rwork0.2217 --
obs0.225 35743 94.92 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.704 Å2 / ksol: 0.313 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.6417 Å20 Å20 Å2
2--1.5251 Å2-0 Å2
3---1.1167 Å2
Refinement stepCycle: LAST / Resolution: 2.869→43.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6830 0 104 0 6934
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017123
X-RAY DIFFRACTIONf_angle_d1.4089572
X-RAY DIFFRACTIONf_dihedral_angle_d17.3422689
X-RAY DIFFRACTIONf_chiral_restr0.0871037
X-RAY DIFFRACTIONf_plane_restr0.0061246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.869-2.97150.37971310.3181865X-RAY DIFFRACTION54
2.9715-3.09050.31592290.26813279X-RAY DIFFRACTION95
3.0905-3.23110.32362340.25523496X-RAY DIFFRACTION100
3.2311-3.40140.29742490.24483460X-RAY DIFFRACTION100
3.4014-3.61440.33822000.24113533X-RAY DIFFRACTION100
3.6144-3.89330.26792050.23573528X-RAY DIFFRACTION100
3.8933-4.28480.25432230.20363533X-RAY DIFFRACTION100
4.2848-4.9040.23782540.16943524X-RAY DIFFRACTION100
4.904-6.17560.25762210.20213614X-RAY DIFFRACTION100
6.1756-43.06180.2842330.24033732X-RAY DIFFRACTION99
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)
11.4048-0.8374-0.02063.8599-1.07891.28240.31570.12410.2598-0.4629-0.1834-0.80390.52360.23780.01210.24120.0472-0.08250.29170.03970.188213.44311.442123.014
20.0758-0.13930.05680.4540.33560.31850.3141-0.038-0.68640.40060.2010.94230.0286-0.1227-0.24820.0501-0.1274-0.00860.62590.37640.7771-30.112121.4998-7.8984
32.2258-0.91970.75891.1197-0.85991.3988-0.0293-0.11520.38960.26930.183-0.0304-0.2712-0.1991-0.06360.1946-0.0068-0.00430.22240.19830.2946-8.511839.9569-18.2742
42.1003-0.9746-0.58421.5299-0.17250.1981-0.10340.53190.75471.1216-0.27140.3385-0.8302-0.08210.32831.12560.14830.08871.5472-0.36491.0328-11.847634.344112.178
50.759-0.2583-0.02180.37910.1540.28740.21-0.21590.1306-0.4696-0.1962-0.2904-0.01220.05890.14170.41840.0990.0730.26530.14170.3701-62.818276.1868-27.7196
60.32510.0954-0.06480.7507-1.05141.57540.07220.3230.0398-1.3948-0.72850.0752-0.39210.8743-0.05691.30830.2036-0.40040.494-0.05130.2644-86.35393.267-50.4192
70.4876-0.0863-0.26740.08550.20420.389-0.0245-0.5782-0.29310.36630.42330.26580.402-0.47350.27860.5872-0.22770.1490.6685-0.01031.4047-106.554585.8402-80.4326
80.6369-0.07610.8550.30820.2341.43310.85340.5652-0.4158-0.0968-0.0536-0.15510.0520.5814-0.88081.2988-0.17070.07721.0751-0.02891.9244-120.151768.5702-74.1476
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1:57 OR RESID 1005:1008)
2X-RAY DIFFRACTION2CHAIN A AND RESID 58:118
3X-RAY DIFFRACTION3CHAIN A AND (RESID 119:536 OR RESID 1001:1003 OR RESID 601:608)
4X-RAY DIFFRACTION4CHAIN A AND (RESID 537:591 OR RESID 1009:1010)
5X-RAY DIFFRACTION5CHAIN A AND RESID 620:681
6X-RAY DIFFRACTION6CHAIN A AND RESID 682:744
7X-RAY DIFFRACTION7CHAIN A AND RESID 750:832
8X-RAY DIFFRACTION8CHAIN A AND RESID 833:913

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