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- PDB-9ekd: Structure of a C1r Zymogen Fragment Bound to SALO -

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Basic information

Entry
Database: PDB / ID: 9ekd
TitleStructure of a C1r Zymogen Fragment Bound to SALO
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 / innate immune response / serine-type endopeptidase activity / 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 / 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 ...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 / 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-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: 3.28 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: To Be Published
Title: Complement Evasion by Blocking Activation of the C1r Zymogen
Authors: Duan, H. / Geisbrecht, B.V.
History
DepositionDec 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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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)117,6464
Polymers117,6464
Non-polymers00
Water00
1
A: Salivary anti-complement protein
C: Complement C1r subcomponent


Theoretical massNumber of molelcules
Total (without water)58,8232
Polymers58,8232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-9 kcal/mol
Surface area24080 Å2
MethodPISA
2
B: Salivary anti-complement protein
D: Complement C1r subcomponent


Theoretical massNumber of molelcules
Total (without water)58,8232
Polymers58,8232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-8 kcal/mol
Surface area24010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.831, 117.831, 190.582
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: 12205.401 Da / Num. of mol.: 2
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 / Fragment: residues 308-705 / 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 ligand of interestY
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: 3.25 Å3/Da / Density % sol: 62.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M BIS-TRIS (pH 5.6), 0.2 M ammonium sulfate, 20% (w/v) PEG-3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.28→50 Å / Num. obs: 23755 / % possible obs: 100 % / Redundancy: 17.7 % / CC1/2: 0.93 / CC star: 0.982 / Rmerge(I) obs: 0.226 / Rpim(I) all: 0.055 / Rrim(I) all: 0.233 / Χ2: 1.023 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2
3.3-3.4215.22.21823280.5140.8240.5852.2951.048
3.42-3.5515.41.63623460.680.90.4291.6921.052
3.55-3.7216.41.06923190.8490.9580.271.1031.067
3.72-3.9118.30.69323510.9310.9820.1650.7121.013
3.91-4.1619.90.45523460.9680.9920.1040.4671.017
4.16-4.4819.70.31523460.9790.9950.0720.3231.025
4.48-4.9319.30.2423840.9880.9970.0560.2471.011
4.93-5.6418.90.20823860.9880.9970.0490.2141.018
5.64-7.115.90.1624010.9910.9980.0410.1650.996
7.1-5018.30.16225480.9920.9980.0390.1670.999

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5127refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.28→49.29 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2865 1996 8.5 %
Rwork0.2422 --
obs0.2459 23486 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.28→49.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7644 0 0 0 7644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0017826
X-RAY DIFFRACTIONf_angle_d0.42710598
X-RAY DIFFRACTIONf_dihedral_angle_d9.9932904
X-RAY DIFFRACTIONf_chiral_restr0.041103
X-RAY DIFFRACTIONf_plane_restr0.0031399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.28-3.370.3891150.32191265X-RAY DIFFRACTION83
3.37-3.460.35991420.31821509X-RAY DIFFRACTION98
3.46-3.560.38451420.33481496X-RAY DIFFRACTION98
3.56-3.670.35781480.28481526X-RAY DIFFRACTION98
3.67-3.80.31321370.28051516X-RAY DIFFRACTION98
3.81-3.960.3351450.27111516X-RAY DIFFRACTION99
3.96-4.140.33811450.25141533X-RAY DIFFRACTION99
4.14-4.360.29111470.24581562X-RAY DIFFRACTION100
4.36-4.630.26291420.21741546X-RAY DIFFRACTION100
4.63-4.980.24081450.21171572X-RAY DIFFRACTION100
4.99-5.480.26321460.23641560X-RAY DIFFRACTION100
5.49-6.280.25661450.27181581X-RAY DIFFRACTION100
6.28-7.90.30531460.24641616X-RAY DIFFRACTION100
7.91-49.290.26391510.21121692X-RAY DIFFRACTION100
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)
16.67663.11473.58585.76754.04133.30950.28910.38152.37240.2635-1.2770.8389-0.6955-1.76911.02671.51360.28580.4331.87980.70852.9445-4.926-30.6713.821
28.4114.10551.27264.0962.84033.1764-0.42191.2091.1426-1.25451.06033.1422-0.9068-0.089-0.2781.1841-0.1209-0.04051.26710.01491.963-4.95-44.9745.34
39.18614.66245.1262.70253.80897.4002-0.28422.3323-2.41730.19062.2829-0.82880.13052.1661-1.61871.5464-0.4053-0.05081.9861-0.00842.12944.26-39.03218.315
47.381.59841.13976.0643-0.33387.9746-0.4795-1.3979-1.86171.06511.18311.0313-0.4662-0.2118-0.26270.6130.27260.23940.92970.07941.037-5.461-36.25221.881
51.308-0.2687-0.2544.2317-1.58951.3121-0.4477-1.0590.73960.21860.61913.04190.0764-0.819-0.1910.57270.25990.07831.27670.09661.7617-10.574-33.67111.871
66.6985-2.7791-2.57511.79530.77511.4829-0.2849-0.1196-0.6079-0.07210.13590.22120.39710.1410.1630.88820.1650.08361.12790.15730.914250.841-52.666-4.796
73.89921.67051.0194.0072-0.10273.9095-0.32320.24681.2894-0.4920.20780.3897-0.5501-0.14770.06360.75710.0923-0.00121.2910.47091.262219.232-23.36-5.522
88.6927-3.2650.9313.6857-0.34713.6021.11882.07910.4608-0.5425-0.9453-0.1153-0.638-0.2511-0.19660.8840.14090.03161.81830.59781.38442.633-24.448-10.402
98.34751.4006-1.09777.71560.41797.16940.33661.7892-0.2322-1.75610.3661-0.10190.17680.6372-0.79531.08020.0725-0.0671.77460.15781.000313.813-26.845-12.938
105.33051.607-2.09819.2468-2.62567.13110.9071-0.6771-1.32490.95950.18610.17671.5958-0.526-0.92951.7786-0.3853-0.28291.3556-0.10391.65630.224-75.43827.682
117.865-3.37170.5645.4516-0.41491.10790.72640.6057-2.01750.04620.25720.4623-0.09911.8008-0.85891.6663-0.4047-0.29812.27680.17941.47719.782-75.66232.953
127.22644.19795.70541.77322.80464.43110.33130.5658-0.8210.43660.25-0.34830.36160.3143-0.64390.9869-0.0258-0.28551.0476-0.11080.837268.471-38.53857.65
134.40612.21432.20213.2521.83076.9588-0.2190.87440.1555-0.53490.420.3201-0.019-0.3699-0.14670.6981-0.1675-0.03561.28450.09680.913133.458-45.00527.681
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 24:42 )A24 - 42
2X-RAY DIFFRACTION2( CHAIN A AND RESID 43:55 )A43 - 55
3X-RAY DIFFRACTION3( CHAIN A AND RESID 56:66 )A56 - 66
4X-RAY DIFFRACTION4( CHAIN A AND RESID 67:86 )A67 - 86
5X-RAY DIFFRACTION5( CHAIN A AND RESID 87:112 )A87 - 112
6X-RAY DIFFRACTION6( CHAIN C AND RESID 308:465 )C308 - 465
7X-RAY DIFFRACTION7( CHAIN C AND RESID 466:599 )C466 - 599
8X-RAY DIFFRACTION8( CHAIN C AND RESID 600:649 )C600 - 649
9X-RAY DIFFRACTION9( CHAIN C AND RESID 650:686 )C650 - 686
10X-RAY DIFFRACTION10( CHAIN B AND RESID 24:104 )B24 - 104
11X-RAY DIFFRACTION11( CHAIN B AND RESID 105:112 )B105 - 112
12X-RAY DIFFRACTION12( CHAIN D AND RESID 308:464 )D308 - 464
13X-RAY DIFFRACTION13( CHAIN D AND RESID 465:686 )D465 - 686

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