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- PDB-8w18: The crystal structure of the Michaelis-Menten complex of a C1s/C1... -

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Basic information

Entry
Database: PDB / ID: 8w18
TitleThe crystal structure of the Michaelis-Menten complex of a C1s/C1-INH at 3.94 Angstroms
Components
  • Complement C1s subcomponent heavy chain
  • Complement C1s subcomponent light chain
  • Plasma protease C1 inhibitor
KeywordsIMMUNE SYSTEM / complement / C1s / C1 esterase inhibitor / Michaelis complex / reactive center loop / exosite
Function / homology
Function and homology information


complement subcomponent C_overbar_1s_ / negative regulation of complement activation, lectin pathway / Defective SERPING1 causes hereditary angioedema / blood circulation / Classical antibody-mediated complement activation / Initial triggering of complement / complement activation, classical pathway / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / platelet alpha granule lumen ...complement subcomponent C_overbar_1s_ / negative regulation of complement activation, lectin pathway / Defective SERPING1 causes hereditary angioedema / blood circulation / Classical antibody-mediated complement activation / Initial triggering of complement / complement activation, classical pathway / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / platelet alpha granule lumen / Regulation of Complement cascade / serine-type endopeptidase inhibitor activity / blood coagulation / Platelet degranulation / : / blood microparticle / endoplasmic reticulum lumen / 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 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family ...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 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / 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 / 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
Plasma protease C1 inhibitor / Complement C1s subcomponent
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.94 Å
AuthorsGarrigues, R.J. / Garcia, B.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: J Immunol. / Year: 2024
Title: The Crystal Structure of the Michaelis-Menten Complex of C1 Esterase Inhibitor and C1s Reveals Novel Insights into Complement Regulation.
Authors: Garrigues, R.J. / Garrison, M.P. / Garcia, B.L.
History
DepositionFeb 15, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _pdbx_audit_support.funding_organization
Revision 1.2Sep 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
I: Plasma protease C1 inhibitor
B: Complement C1s subcomponent light chain
A: Complement C1s subcomponent heavy chain


Theoretical massNumber of molelcules
Total (without water)88,2543
Polymers88,2543
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-22 kcal/mol
Surface area35240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.628, 168.628, 88.342
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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Components

#1: Protein Plasma protease C1 inhibitor / C1 Inh / C1Inh / C1 esterase inhibitor / C1-inhibiting factor / Serpin G1


Mass: 43997.434 Da / Num. of mol.: 1 / Fragment: residues 111-500
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPING1, C1IN, C1NH / Production host: Escherichia coli (E. coli) / References: UniProt: P05155
#2: Protein Complement C1s subcomponent light chain


Mass: 27668.547 Da / Num. of mol.: 1 / Mutation: S632A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C1S / Production host: Escherichia coli (E. coli) / References: UniProt: P09871
#3: Protein Complement C1s subcomponent heavy chain


Mass: 16588.488 Da / Num. of mol.: 1 / Fragment: Sushi domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C1S / Production host: Escherichia coli (E. coli) / References: UniProt: P09871
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: 3.56 Å3/Da / Density % sol: 65.43 % / Description: blocks
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1 M L-Proline, 0.1M HEPES (pH 6.5), and 12% PEG 3,350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.94→49.42 Å / Num. obs: 11775 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 145.32 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.127 / Net I/σ(I): 6.9
Reflection shellResolution: 3.94→4.15 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3267 / CC1/2: 0.446 / Rpim(I) all: 0.776 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.94→47.42 Å / SU ML: 0.7373 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.1233
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2807 1173 10 %
Rwork0.262 10560 -
obs0.2639 11733 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 161.56 Å2
Refinement stepCycle: LAST / Resolution: 3.94→47.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6029 0 0 0 6029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00486172
X-RAY DIFFRACTIONf_angle_d0.73338379
X-RAY DIFFRACTIONf_chiral_restr0.0526939
X-RAY DIFFRACTIONf_plane_restr0.00371077
X-RAY DIFFRACTIONf_dihedral_angle_d14.00542277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.94-4.120.44821440.41781300X-RAY DIFFRACTION99.79
4.12-4.340.3991420.3581276X-RAY DIFFRACTION99.93
4.34-4.610.29521450.31581300X-RAY DIFFRACTION100
4.61-4.960.33321440.31711303X-RAY DIFFRACTION100
4.96-5.460.35081450.29471298X-RAY DIFFRACTION99.93
5.46-6.250.31661470.29021321X-RAY DIFFRACTION100
6.25-7.870.26671470.24181337X-RAY DIFFRACTION99.87
7.87-47.420.18971590.17961425X-RAY DIFFRACTION99.69

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