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- PDB-5ubm: Crystal structure of human C1s in complex with inhibitor gigastasin -

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Basic information

Entry
Database: PDB / ID: 5ubm
TitleCrystal structure of human C1s in complex with inhibitor gigastasin
Components
  • (Complement C1s subcomponent) x 2
  • Gigastasin
KeywordsIMMUNE SYSTEM/INHIBITOR / Complement system C1s protease inhibitor complex / IMMUNE SYSTEM-INHIBITOR complex
Function / homology
Function and homology information


complement subcomponent C_overbar_1s_ / Classical antibody-mediated complement activation / Initial triggering of complement / complement activation, classical pathway / Regulation of Complement cascade / blood microparticle / innate immune response / serine-type endopeptidase activity / calcium ion binding / proteolysis ...complement subcomponent C_overbar_1s_ / Classical antibody-mediated complement activation / Initial triggering of complement / complement activation, classical pathway / Regulation of Complement cascade / blood microparticle / innate immune response / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Peptidase S1A, complement C1r/C1S/mannan-binding / Complement Module, domain 1 / Complement Module; domain 1 / 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) ...Peptidase S1A, complement C1r/C1S/mannan-binding / Complement Module, domain 1 / Complement Module; domain 1 / 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 / Ribbon / 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 / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Complement C1s subcomponent
Similarity search - Component
Biological speciesHaementeria ghilianii (Amazon leech)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPang, S.S. / Whisstock, J.C.
CitationJournal: J. Immunol. / Year: 2017
Title: The Structural Basis for Complement Inhibition by Gigastasin, a Protease Inhibitor from the Giant Amazon Leech.
Authors: Pang, S.S. / Wijeyewickrema, L.C. / Hor, L. / Tan, S. / Lameignere, E. / Conway, E.M. / Blom, A.M. / Mohlin, F.C. / Liu, X. / Payne, R.J. / Whisstock, J.C. / Pike, R.N.
History
DepositionDec 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 2.3Nov 6, 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 C1s subcomponent
B: Complement C1s subcomponent
I: Gigastasin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2534
Polymers60,8293
Non-polymers4241
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-13 kcal/mol
Surface area24860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.350, 89.350, 146.871
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-739-

HOH

21B-2120-

HOH

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Components

#1: Protein Complement C1s subcomponent / C1 esterase / Complement component 1 subcomponent s


Mass: 27841.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: blood plasma
References: UniProt: P09871, complement subcomponent C_overbar_1s_
#2: Protein Complement C1s subcomponent / C1 esterase / Complement component 1 subcomponent s


Mass: 16882.857 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: blood plasma
References: UniProt: P09871, complement subcomponent C_overbar_1s_
#3: Protein Gigastasin


Mass: 16104.122 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haementeria ghilianii (Amazon leech) / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): BTI-TN-5B1-4
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M Bis-Tris, pH 5.5, 25 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→53.3 Å / Num. obs: 24136 / % possible obs: 100 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.8
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
SCALAdata scaling
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ELV

1elv


Resolution: 2.5→41.372 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.71
RfactorNum. reflection% reflection
Rfree0.2223 1231 5.11 %
Rwork0.1767 --
obs0.179 24091 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→41.372 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3810 0 0 126 3936
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043920
X-RAY DIFFRACTIONf_angle_d0.8725300
X-RAY DIFFRACTIONf_dihedral_angle_d14.2531406
X-RAY DIFFRACTIONf_chiral_restr0.036560
X-RAY DIFFRACTIONf_plane_restr0.004692
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.60010.34231310.26732510X-RAY DIFFRACTION100
2.6001-2.71840.29971370.24642502X-RAY DIFFRACTION100
2.7184-2.86170.25221380.21692479X-RAY DIFFRACTION100
2.8617-3.04090.26731430.21152488X-RAY DIFFRACTION100
3.0409-3.27560.25141260.20342542X-RAY DIFFRACTION100
3.2756-3.60510.22231190.17712550X-RAY DIFFRACTION100
3.6051-4.12640.20151550.15532510X-RAY DIFFRACTION100
4.1264-5.19720.1711580.13622569X-RAY DIFFRACTION100
5.1972-41.37750.21511240.16162710X-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)
13.14830.6327-1.26991.56960.72155.50320.1540.02150.2884-0.0106-0.09150.0697-0.23110.2103-0.04010.24420.049-0.0110.18660.01620.290122.52934.731720.2774
25.0418-0.25730.02556.2968-2.73088.17210.13430.36150.4732-0.1221-0.08360.054-0.226-0.5211-0.08360.30170.11220.03240.1984-0.01810.266818.016437.08224.794
33.2356-1.1530.61163.7225-0.49084.58780.0343-0.2129-0.37450.49070.08890.13560.29490.1692-0.12710.29550.0057-0.01610.22990.00120.271821.117924.433124.3991
44.619-3.9472-1.72638.87731.23864.36750.3481-0.08290.57780.0108-0.16940.0374-0.40190.6399-0.23650.2007-0.0213-0.01350.4216-0.02040.276934.429533.420415.4406
52.1048-1.067-1.18012.2991-1.67083.97980.346-0.1887-0.22590.37910.0992-0.37370.53471.6206-0.15940.55840.2714-0.26130.6622-0.10870.496639.580920.790725.582
67.24914.782-5.28459.0309-8.05168.68460.37280.6355-1.0134-1.4047-0.3881-1.65061.80051.95540.3930.50710.1927-0.00280.7303-0.20920.589141.902124.857515.3818
72.6452-0.6429-0.71753.31250.28484.74070.08810.0365-0.31660.06740.0498-0.22020.27550.5-0.18140.29170.0942-0.06110.3086-0.0220.311130.417923.276620.1923
85.3886-5.4307-4.71395.5764.81744.1602-0.00790.0664-1.06210.51-0.1231.4610.9762-0.71880.25590.4912-0.08030.04220.36120.06260.52911.645820.588729.1769
93.5095-2.09860.76513.25032.03563.28370.01770.45660.5092-1.3286-0.87420.4086-0.6392-0.55590.97620.8570.091-0.18361.08830.03420.534-48.65458.72721.3445
107.525-2.0505-1.75754.8104-1.03516.7123-0.08960.81460.4669-0.282-0.2419-0.207-0.49770.42340.28550.30340.0141-0.03650.39380.02180.2753-40.433410.68587.6207
117.80024.4075.23995.59253.16874.4594-0.30830.28190.9684-0.27870.4130.6126-0.2868-0.3823-0.23060.3140.01070.01150.66290.17040.4689-10.337823.14194.3259
127.15182.26051.05861.8308-0.10711.55050.05240.2799-0.74210.06880.2674-0.16140.3277-0.0824-0.2710.29240.0594-0.00250.3949-0.01630.34674.229920.00017.7336
135.33760.4360.76670.04410.07320.10660.13610.5962-0.3739-0.18420.0417-0.2319-0.09122.3345-0.01530.56430.01680.02751.4529-0.34620.862553.984133.604712.2904
146.3368-4.7822-5.77623.71654.46225.36931.16820.24120.2677-0.930.3623-1.208-1.27260.5421-1.38370.8082-0.37860.31671.54-0.47371.164456.361439.37069.6284
159.2633-0.3445-1.27748.1195-2.33398.4438-0.65870.74431.0041-0.23650.45-1.1706-0.36941.56250.35470.6246-0.25050.1270.8614-0.24060.957549.798445.482428.0264
167.5391.82681.60693.2780.28593.52210.1674-0.19320.5176-0.17770.2384-1.09380.14271.837-0.3160.4409-0.0065-0.08431.0992-0.220.797250.500236.474827.3835
178.59694.57186.02917.1246-0.58459.5001-0.2086-0.22920.85180.34130.3932-0.0612-0.60370.6937-0.26830.5404-0.07720.00030.4851-0.18440.462736.974443.521234.6722
185.34841.12363.42613.7191.72452.8177-0.11851.17640.9572-0.8690.0503-0.0521-1.13710.63870.07510.7151-0.13560.17420.66380.00020.710639.85452.589522.8112
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 438:492)
2X-RAY DIFFRACTION2(chain A and resid 493:514)
3X-RAY DIFFRACTION3(chain A and resid 515:559)
4X-RAY DIFFRACTION4(chain A and resid 560:583)
5X-RAY DIFFRACTION5(chain A and resid 584:617)
6X-RAY DIFFRACTION6(chain A and resid 618:625)
7X-RAY DIFFRACTION7(chain A and resid 626:672)
8X-RAY DIFFRACTION8(chain A and resid 673:684)
9X-RAY DIFFRACTION9(chain B and resid 290:299)
10X-RAY DIFFRACTION10(chain B and resid 300:354)
11X-RAY DIFFRACTION11(chain B and resid 355:388)
12X-RAY DIFFRACTION12(chain B and resid 389:436)
13X-RAY DIFFRACTION13(chain I and resid 3:20)
14X-RAY DIFFRACTION14(chain I and resid 21:31)
15X-RAY DIFFRACTION15(chain I and resid 32:43)
16X-RAY DIFFRACTION16(chain I and resid 44:65)
17X-RAY DIFFRACTION17(chain I and resid 66:92)
18X-RAY DIFFRACTION18(chain I and resid 93:119)

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