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- PDB-6f1c: C1rC1s complex -

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Basic information

Entry
Database: PDB / ID: 6f1c
TitleC1rC1s complex
Components
  • Complement C1r subcomponent
  • Complement C1s subcomponent
KeywordsHYDROLASE / CUB domain / EGF-like domain / complement / C1r-C1s
Function / homology
Function and homology information


complement subcomponent C_overbar_1r_ / complement subcomponent C_overbar_1s_ / zymogen activation / Classical antibody-mediated complement activation / Initial triggering of complement / molecular sequestering activity / complement activation, classical pathway / serine-type peptidase activity / Regulation of Complement cascade / blood microparticle ...complement subcomponent C_overbar_1r_ / complement subcomponent C_overbar_1s_ / zymogen activation / Classical antibody-mediated complement activation / Initial triggering of complement / molecular sequestering activity / complement activation, classical pathway / serine-type peptidase activity / Regulation of Complement cascade / blood microparticle / immune response / innate immune response / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Peptidase S1A, complement C1r/C1S/mannan-binding / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. ...Peptidase S1A, complement C1r/C1S/mannan-binding / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Coagulation Factor Xa inhibitory site / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain signature 2. / EGF-like domain / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Complement C1r subcomponent / Complement C1s subcomponent
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.2 Å
AuthorsAlmitairi, J.O.M. / Venkatraman Girija, U. / Furze, C.M. / Simpson-Gray, X. / Badakshi, F. / Marshall, J.E. / Mitchell, D.A. / Moody, P.C.E. / Wallis, R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G1000191/1 United Kingdom
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structure of the C1r-C1s interaction of the C1 complex of complement activation.
Authors: Almitairi, J.O.M. / Venkatraman Girija, U. / Furze, C.M. / Simpson-Gray, X. / Badakshi, F. / Marshall, J.E. / Schwaeble, W.J. / Mitchell, D.A. / Moody, P.C.E. / Wallis, R.
History
DepositionNov 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_audit_support.funding_organization
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 / 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_conn_type / 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 / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2Nov 13, 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
A: Complement C1r subcomponent
C: Complement C1r subcomponent
D: Complement C1s subcomponent
B: Complement C1s subcomponent
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,94928
Polymers128,7314
Non-polymers4,21824
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11020 Å2
ΔGint-72 kcal/mol
Surface area60270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.779, 124.265, 195.499
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain B and resid 2 through 276)
21(chain D and resid 2 through 276)
12(chain A and resid 4 through 290)
22chain C

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROPROPRO(chain B and resid 2 through 276)BD2 - 2762 - 276
21PROPROPROPRO(chain D and resid 2 through 276)DC2 - 2762 - 276
12ILEILEILEILE(chain A and resid 4 through 290)AA4 - 2904 - 290
22ILEILEILEILEchain CCB4 - 2904 - 290

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ACDB

#1: Protein Complement C1r subcomponent / Complement component 1 subcomponent r


Mass: 33120.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C1R / Plasmid: pED4 / Cell line (production host): DXB11 / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P00736, complement subcomponent C_overbar_1r_
#2: Protein Complement C1s subcomponent / C1 esterase / Complement component 1 subcomponent s


Mass: 31244.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C1S / Plasmid: pED4 / Cell line (production host): DXB11 / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P09871, complement subcomponent C_overbar_1s_

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Sugars , 4 types, 6 molecules

#3: Polysaccharide beta-D-galactopyranose-(1-4)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...beta-D-galactopyranose-(1-4)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5]/1-1-2-3-4-3/a4-b1_b4-c1_c3-d1_c6-f1_d4-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(4+1)][b-D-Galp]{}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#8: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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

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Non-polymers , 2 types, 18 molecules

#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na

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Details

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: 4.58 Å3/Da / Density % sol: 73.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 12-18% PEG 8000, 100 mM Imidazole at pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 4.2→97.8 Å / Num. obs: 17763 / % possible obs: 99.8 % / Redundancy: 7.6 % / Biso Wilson estimate: 157.84 Å2 / Net I/σ(I): 6.6
Reflection shellResolution: 4.2→4.7 Å

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
EDNAdata collection
Aimlessdata scaling
PHASERphasing
PHENIXdev_2722refinement
PDB_EXTRACT3.22data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LOR

4lor


Resolution: 4.2→97.749 Å / SU ML: 0.67 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.22
RfactorNum. reflection% reflection
Rfree0.305 828 4.67 %
Rwork0.2471 --
obs0.2499 17726 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 405.17 Å2 / Biso mean: 226.7657 Å2 / Biso min: 117.27 Å2
Refinement stepCycle: final / Resolution: 4.2→97.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9003 0 257 0 9260
Biso mean--286.4 --
Num. residues----1130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049539
X-RAY DIFFRACTIONf_angle_d0.90712995
X-RAY DIFFRACTIONf_chiral_restr0.0591384
X-RAY DIFFRACTIONf_plane_restr0.0051701
X-RAY DIFFRACTIONf_dihedral_angle_d12.1995709
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B2649X-RAY DIFFRACTION10.303TORSIONAL
12D2649X-RAY DIFFRACTION10.303TORSIONAL
21A2723X-RAY DIFFRACTION10.303TORSIONAL
22C2723X-RAY DIFFRACTION10.303TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.2-4.46320.42821380.383227732911100
4.4632-4.80780.33651210.31192760288199
4.8078-5.29160.31481340.257727872921100
5.2916-6.05720.30731300.254928342964100
6.0572-7.63090.28271480.25052800294899
7.6309-97.77590.28551570.2032944310199
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)
13.7798-0.51781.10.4511-1.10990.52530.1994-0.5308-0.265-0.2236-0.010.1430.6324-0.2885-01.4132-0.09780.13510.6655-0.13531.479564.3357.612-32.3524
2-0.11740.7341.20410.34162.66391.49110.22160.91830.3315-0.9335-0.6711-0.05450.3179-0.6306-0.00461.5527-0.187-0.09082.2459-0.2031.778928.217621.071711.9938
30.98410.83461.40330.6851-0.57132.4156-0.5557-0.36140.2477-0.19630.7464-0.44220.2299-0.079101.8824-0.3824-0.10362.05690.00261.510612.1256-2.5996-3.7349
40.03761.24090.30260.5556-0.28971.5584-0.0937-0.9241-0.0085-0.1758-0.22250.4981.23670.30280.00181.6722-0.2928-0.17291.54540.15551.50444.279-1.0493-53.5825
50.71781.1592-0.45331.82050.16110.41490.16580.39630.38820.9193-0.33120.15951.01670.46670.00011.56460.02710.12192.36710.04391.532822.8159-15.5386-47.0666
6-0.4091-1.2288-1.6013-2.12520.94860.609-1.2088-0.3121-0.5721-0.2387-0.0273-0.19752.74091.2763-0.00672.8539-0.4440.32523.1834-0.13732.02028.4987-16.7851-21.8914
7-0.05130.0356-0.0444-0.15530.04150.685-0.5136-0.0755-1.8008-0.73891.35790.53321.54250.2851-0.00012.6123-0.32970.40433.86440.29172.542-17.6877-12.51355.215
82.3244-0.67551.44210.0455-0.32190.7498-0.914-0.23610.67650.71810.3945-0.00480.45161.09250.00031.45960.24340.13361.6609-0.21711.500158.035921.02345.3969
90.2148-0.6633-0.0340.6992-0.06250.2033-0.1961-0.4749-2.62161.2295-0.86431.84020.4466-3.78960.00131.35480.14360.23352.31680.03581.938282.109311.9616-20.8511
100.49940.5675-0.4980.8583-0.52990.1958-0.209-0.35970.3771-0.13690.2616-0.53170.05830.5664-0.00011.1740.05060.09122.1121-0.35531.398198.594920.9018-35.4304
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 161 )A5 - 161
2X-RAY DIFFRACTION2chain 'A' and (resid 162 through 291 )A162 - 291
3X-RAY DIFFRACTION3chain 'C' and (resid 5 through 125 )C5 - 125
4X-RAY DIFFRACTION4chain 'C' and (resid 126 through 290 )C126 - 290
5X-RAY DIFFRACTION5chain 'D' and (resid 2 through 96 )D2 - 96
6X-RAY DIFFRACTION6chain 'D' and (resid 97 through 173 )D97 - 173
7X-RAY DIFFRACTION7chain 'D' and (resid 174 through 276 )D174 - 276
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 116 )B2 - 116
9X-RAY DIFFRACTION9chain 'B' and (resid 117 through 158 )B117 - 158
10X-RAY DIFFRACTION10chain 'B' and (resid 159 through 277 )B159 - 277

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