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- PDB-9eke: Structure of a C1r Zymogen Fragment Bound to SALO, Y51F Mutant -

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Basic information

Entry
Database: PDB / ID: 9eke
TitleStructure of a C1r Zymogen Fragment Bound to SALO, Y51F Mutant
Components
  • Complement C1r subcomponent
  • Salivary anti-complement protein
KeywordsIMMUNE SYSTEM / HYDROLASE / complement system / C1r / zymogen / inhibitor
Function / homology
Function and homology information


complement subcomponent C_overbar_1r_ / odorant binding / 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 / toxin activity ...complement subcomponent C_overbar_1r_ / odorant binding / 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 / toxin activity / blood microparticle / immune response / serine-type endopeptidase activity / innate immune response / calcium ion binding / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Peptidase S1A, complement C1r/C1S/mannan-binding / Pheromone/general odorant binding protein superfamily / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / Spermadhesin, CUB domain superfamily / CUB domain profile. / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain ...Peptidase S1A, complement C1r/C1S/mannan-binding / Pheromone/general odorant binding protein superfamily / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / Spermadhesin, CUB domain superfamily / CUB domain profile. / 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-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 / Salivary anti-complement protein
Similarity search - Component
Biological speciesLutzomyia longipalpis (insect)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsDuan, H. / Geisbrecht, B.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM140852 United States
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Blocking activation of the C1r zymogen defines a novel mode of complement inhibition.
Authors: Duan, H. / Wu, W. / Li, P. / Bouyain, S. / Garcia, B.L. / Geisbrecht, B.V.
History
DepositionDec 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Salivary anti-complement protein
C: Complement C1r subcomponent
B: Salivary anti-complement protein
D: Complement C1r subcomponent


Theoretical massNumber of molelcules
Total (without water)117,4544
Polymers117,4544
Non-polymers00
Water00
1
A: Salivary anti-complement protein
C: Complement C1r subcomponent


Theoretical massNumber of molelcules
Total (without water)58,7272
Polymers58,7272
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-12 kcal/mol
Surface area23840 Å2
MethodPISA
2
B: Salivary anti-complement protein
D: Complement C1r subcomponent


Theoretical massNumber of molelcules
Total (without water)58,7272
Polymers58,7272
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-10 kcal/mol
Surface area23730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.810, 117.810, 195.586
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Salivary anti-complement protein / 10.7 kDa salivary protein / LJM19 / Salivary anti-complement from Lu.longipalpis / SALO


Mass: 12109.338 Da / Num. of mol.: 2 / Mutation: Y51F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lutzomyia longipalpis (insect) / Plasmid: pCDNA3.1(+) / Cell line (production host): HEK293(t) / Production host: Homo sapiens (human) / References: UniProt: Q5WPZ4
#2: Protein Complement C1r subcomponent / Complement component 1 subcomponent r


Mass: 46617.547 Da / Num. of mol.: 2 / Mutation: S654A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C1R / Plasmid: pCDNA3.1(+) / Cell line (production host): HEK293(t) / Production host: Homo sapiens (human)
References: UniProt: P00736, complement subcomponent C_overbar_1r_
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: 3.34 Å3/Da / Density % sol: 63.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium citrate tribasic (pH 7.0), 20% (w/v) PEG-3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 3.09→50 Å / Num. obs: 29376 / % possible obs: 100 % / Redundancy: 18.1 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.257 / Rpim(I) all: 0.062 / Rrim(I) all: 0.265 / Χ2: 1.013 / Net I/σ(I): 4.2
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2
3.1-3.2116.93.00828630.4410.7830.7493.1010.982
3.21-3.3418.31.70928770.6690.8950.4081.7581.025
3.34-3.49181.09529070.8260.9510.2641.1271.073
3.49-3.6816.30.91329070.8960.9720.2310.9421.051
3.68-3.9117.40.69928950.9510.9870.1720.721.043
3.91-4.2118.50.44529320.9810.9950.1060.4581.027
4.21-4.6319.50.26529140.9910.9980.0610.2720.992
4.63-5.319.30.18829610.9950.9990.0440.1931.009
5.3-6.6717.90.14829850.9970.9990.0360.1520.982
6.67-5018.90.05831350.99910.0140.060.956

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5127refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→49.36 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 0.24 / Phase error: 30.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2781 2006 7.91 %
Rwork0.2305 --
obs0.2344 25373 86.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→49.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7515 0 0 0 7515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027692
X-RAY DIFFRACTIONf_angle_d0.46210407
X-RAY DIFFRACTIONf_dihedral_angle_d4.0651023
X-RAY DIFFRACTIONf_chiral_restr0.0411086
X-RAY DIFFRACTIONf_plane_restr0.0041372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.170.41161130.34611309X-RAY DIFFRACTION70
3.17-3.250.35441330.33831514X-RAY DIFFRACTION80
3.25-3.350.37691370.31241598X-RAY DIFFRACTION84
3.35-3.460.3441480.29051719X-RAY DIFFRACTION90
3.46-3.580.35971330.29051565X-RAY DIFFRACTION83
3.58-3.730.35511340.29411586X-RAY DIFFRACTION83
3.73-3.890.32561360.25531583X-RAY DIFFRACTION83
3.89-4.10.28591350.23631582X-RAY DIFFRACTION82
4.1-4.360.24631420.20281612X-RAY DIFFRACTION84
4.36-4.690.22181460.1931739X-RAY DIFFRACTION90
4.69-5.160.22611530.18531775X-RAY DIFFRACTION91
5.16-5.910.2731590.22331835X-RAY DIFFRACTION94
5.91-7.440.29361660.22721903X-RAY DIFFRACTION96
7.44-49.360.22581710.18912047X-RAY DIFFRACTION98
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)
13.15712.7439-1.88772.5146-1.02464.4057-0.02380.3032-0.5225-0.38451.055-0.68480.8166-0.6121-1.13240.6592-0.0197-0.28380.9287-0.04461.41123.437334.99595.8415
24.1435-0.2859-2.13287.2367-2.1632.4022-0.31150.3406-0.01970.80440.5396-0.24250.2001-0.081-0.22530.7146-0.0572-0.19280.8455-0.04890.7872.689937.879318.8546
32.45890.0533-0.27536.7927-1.95577.5535-0.1257-0.7481-0.85820.8035-0.3752-1.45710.37511.2086-0.18420.79250.0267-0.360.83170.04921.39287.611330.611215.683
47.6118-3.29682.54312.093-0.51.845-0.3711-0.46810.8913-0.01570.0658-0.2268-0.4148-0.41370.30170.63840.091-0.0760.7645-0.05050.5644-59.798655.6631-6.313
52.7854-0.03950.4572.4834-0.27641.641-0.22670.7319-0.7758-0.40570.3014-0.39570.33210.3192-0.09740.5108-0.0862-0.0130.8837-0.30870.8393-17.11724.2744-3.4792
66.58770.42661.42163.1958-0.55722.46910.05231.0792-0.5412-0.57180.474-1.13110.32620.4197-0.05050.5440.0021-0.01881.1205-0.37950.9197-11.657426.1908-7.9011
73.82925.35451.37348.58924.27825.524-0.37880.43482.3415-0.3231-0.1746-0.3248-1.5267-0.6884-0.0261.15940.0449-0.13060.96160.30161.6993-34.671869.670223.0168
84.50142.58545.29324.30073.97868.90641.0318-1.29021.36830.6129-0.25080.0749-0.7219-0.72220.16441.28860.0330.5690.81370.01391.1906-30.663379.179235.6576
98.1396-0.292-0.32796.6171-4.08574.24910.5197-0.18172.1871-0.3042-0.37450.4372-0.54940.4062-0.08431.3777-0.56920.07620.8910.01581.2593-27.682976.24623.7377
105.43073.0964-4.38271.9203-2.25593.28110.1970.0920.63830.21220.15830.5182-0.0245-0.0167-0.53450.5575-0.00030.20440.53140.04760.6487-69.448439.635159.6901
114.06350.7499-3.00092.9311-0.67915.6308-0.05860.4490.1472-0.18160.29130.04030.157-0.1932-0.17170.3681-0.052-0.04810.5039-0.01240.3536-35.200844.60929.1954
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 55 )
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 93 )
3X-RAY DIFFRACTION3chain 'A' and (resid 94 through 112 )
4X-RAY DIFFRACTION4chain 'C' and (resid 308 through 449 )
5X-RAY DIFFRACTION5chain 'C' and (resid 450 through 636 )
6X-RAY DIFFRACTION6chain 'C' and (resid 637 through 703 )
7X-RAY DIFFRACTION7chain 'B' and (resid 24 through 55 )
8X-RAY DIFFRACTION8chain 'B' and (resid 56 through 86 )
9X-RAY DIFFRACTION9chain 'B' and (resid 87 through 112 )
10X-RAY DIFFRACTION10chain 'D' and (resid 308 through 481 )
11X-RAY DIFFRACTION11chain 'D' and (resid 482 through 703 )

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