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- PDB-4djz: Catalytic fragment of masp-1 in complex with its specific inhibit... -

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Basic information

Entry
Database: PDB / ID: 4djz
TitleCatalytic fragment of masp-1 in complex with its specific inhibitor developed by directed evolution on sgci scaffold
Components
  • Mannan-binding lectin serine protease 1 heavy chain
  • Mannan-binding lectin serine protease 1 light chain
  • Protease inhibitor SGPI-2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / in vitro evolution / specific inhibitor / hydrolase / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / negative regulation of complement activation / complement activation, lectin pathway / Scavenging by Class A Receptors / Initial triggering of complement / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase inhibitor activity / calcium-dependent protein binding / peptidase activity ...Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / negative regulation of complement activation / complement activation, lectin pathway / Scavenging by Class A Receptors / Initial triggering of complement / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase inhibitor activity / calcium-dependent protein binding / peptidase activity / serine-type endopeptidase activity / calcium ion binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / proteolysis / extracellular space / extracellular region / nucleoplasm / identical protein binding / cytosol
Similarity search - Function
Protease inhibitor with pacifastin repeats / Pacifastin domain / Pacifastin domain superfamily / Pacifastin inhibitor (LCMII) / Pacifastin domain profile. / 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. ...Protease inhibitor with pacifastin repeats / Pacifastin domain / Pacifastin domain superfamily / Pacifastin inhibitor (LCMII) / Pacifastin domain profile. / 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 / 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 / EGF-like domain signature 2. / EGF-like domain / Ribbon / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine 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
Serine protease inhibitor I/II / Mannan-binding lectin serine protease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Schistocerca gregaria (desert locust)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHeja, D. / Harmat, V. / Fodor, K. / Wilmanns, M. / Dobo, J. / Kekesi, K.A. / Zavodszky, P. / Gal, P. / Pal, G.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Monospecific Inhibitors Show That Both Mannan-binding Lectin-associated Serine Protease-1 (MASP-1) and -2 Are Essential for Lectin Pathway Activation and Reveal Structural Plasticity of MASP-2.
Authors: Heja, D. / Harmat, V. / Fodor, K. / Wilmanns, M. / Dobo, J. / Kekesi, K.A. / Zavodszky, P. / Gal, P. / Pal, G.
History
DepositionFeb 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Database references
Revision 1.2Jun 27, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_ref_seq_dif.details
Revision 1.4Nov 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: Mannan-binding lectin serine protease 1 heavy chain
B: Mannan-binding lectin serine protease 1 light chain
C: Mannan-binding lectin serine protease 1 heavy chain
D: Mannan-binding lectin serine protease 1 light chain
H: Protease inhibitor SGPI-2
I: Protease inhibitor SGPI-2


Theoretical massNumber of molelcules
Total (without water)99,2526
Polymers99,2526
Non-polymers00
Water362
1
A: Mannan-binding lectin serine protease 1 heavy chain
B: Mannan-binding lectin serine protease 1 light chain
H: Protease inhibitor SGPI-2


Theoretical massNumber of molelcules
Total (without water)49,6263
Polymers49,6263
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-23 kcal/mol
Surface area20940 Å2
MethodPISA
2
C: Mannan-binding lectin serine protease 1 heavy chain
D: Mannan-binding lectin serine protease 1 light chain
I: Protease inhibitor SGPI-2


Theoretical massNumber of molelcules
Total (without water)49,6263
Polymers49,6263
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-25 kcal/mol
Surface area20530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.327, 98.404, 155.531
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22C
13A
23C
14B
24D
15H
25I

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRSERSER5AA297 - 3284 - 35
211THRTHRSERSER5CC297 - 3284 - 35
121ASPASPILEILE5AA343 - 36450 - 71
221ASPASPILEILE5CC343 - 36450 - 71
112VALVALSERSER5AA365 - 38172 - 88
212VALVALSERSER5CC365 - 38172 - 88
122THRTHRMETMET5AA387 - 40494 - 111
222THRTHRMETMET5CC387 - 40494 - 111
132GLYGLYPROPRO5AA410 - 434117 - 141
232GLYGLYPROPRO5CC410 - 434117 - 141
113CYSCYSSERSER5AA436 - 442143 - 149
213CYSCYSSERSER5CC436 - 442143 - 149
114ILEILETHRTHR5BB449 - 4591 - 11
214ILEILETHRTHR5DD449 - 4591 - 11
124THRTHRVALVAL1BB460 - 68012 - 232
224THRTHRVALVAL1DD460 - 68012 - 232
134TYRTYRASNASN5BB681 - 699233 - 251
234TYRTYRASNASN5DD681 - 699233 - 251
115PHEPHEARGARG5HE13 - 2113 - 21
215PHEPHEARGARG5IF13 - 2113 - 21
125ALAALACYSCYS5HE29 - 3629 - 36
225ALAALACYSCYS5IF29 - 3629 - 36

NCS ensembles :
ID
1
2
3
4
5

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.995668, 0.019617, 0.090887), (-0.011109, 0.995586, -0.093189), (-0.092314, 0.091776, 0.991491)15.23153, 35.60927, -26.43845
DetailsThe asymmetric unit contains two complexes of the activated MASP-1 fragment and SGMI-1. The two chains of the MASP-1 fragment are conneced by a disulphide bridge. Complex 1: chains A,B and I; complex 2: chains C,D and H.

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Components

#1: Protein Mannan-binding lectin serine protease 1 heavy chain / Mannan-binding lectin serine protease 1 / Complement factor MASP-3 / Complement-activating ...Mannan-binding lectin serine protease 1 / Complement factor MASP-3 / Complement-activating component of Ra-reactive factor / Mannose-binding lectin-associated serine protease 1 / MASP-1 / Mannose-binding protein-associated serine protease / Ra-reactive factor serine protease p100 / RaRF / Serine protease 5


Mass: 17508.240 Da / Num. of mol.: 2 / Fragment: Sushi domain residues 298-448
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRARF, CRARF1, MASP1, PRSS5 / Plasmid: PET-17B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS
References: UniProt: P48740, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Antibody Mannan-binding lectin serine protease 1 light chain / Mannan-binding lectin serine protease 1 / Complement factor MASP-3 / Complement-activating ...Mannan-binding lectin serine protease 1 / Complement factor MASP-3 / Complement-activating component of Ra-reactive factor / Mannose-binding lectin-associated serine protease 1 / MASP-1 / Mannose-binding protein-associated serine protease / Ra-reactive factor serine protease p100 / RaRF / Serine protease 5


Mass: 28028.900 Da / Num. of mol.: 2 / Fragment: Peptidase S1 domain residues 449-699
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRARF, CRARF1, MASP1, PRSS5 / Plasmid: PET-17B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS
References: UniProt: P48740, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#3: Protein/peptide Protease inhibitor SGPI-2 / Protease inhibitor SGPI-2 / Schistocerca gregaria chymotrypsin inhibitor / SGCI


Mass: 4088.627 Da / Num. of mol.: 2 / Mutation: A30F,L33R,A35L,P37Y
Source method: isolated from a genetically manipulated source
Details: expressed as MBP fusion protein / Source: (gene. exp.) Schistocerca gregaria (desert locust) / Gene: Y09605.1 / Plasmid: PMAL-P2G, PMAL-TEV-SGPI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 STAR / References: UniProt: O46162
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.75 Å3/Da / Density % sol: 55.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Hepes, 25% PEG1000, 0.3M NaNO3, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97942 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2011 / Details: mirror
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 3.2→46.91 Å / Num. all: 18731 / Num. obs: 18731 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -6 / Redundancy: 6.8 % / Rmerge(I) obs: 0.238 / Net I/σ(I): 7.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
3.2-3.377.10.9252.326831100
10.12-46.915.60.06616.4667198.7

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries: 2XTT (structure of SGPI-1) and 3GOV

2xtt

3gov


Resolution: 3.2→46.91 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.838 / SU B: 57.255 / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.54 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS WERE NOT ADDED TO THE MODEL
RfactorNum. reflection% reflectionSelection details
Rfree0.27414 951 5.1 %RANDOM
Rwork0.22808 ---
all0.23045 17687 --
obs0.23045 17687 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.858 Å2
Baniso -1Baniso -2Baniso -3
1--3.99 Å2-0 Å20 Å2
2---0.29 Å20 Å2
3---4.28 Å2
Refinement stepCycle: LAST / Resolution: 3.2→46.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6444 0 0 2 6446
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.026654
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0361.9469103
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5835865
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70124.286266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.91315966
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0751526
X-RAY DIFFRACTIONr_chiral_restr0.070.21008
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215126
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A216MEDIUM POSITIONAL0.260.5
1A171LOOSE POSITIONAL0.535
1A216MEDIUM THERMAL1.732
1A171LOOSE THERMAL1.8710
2A240MEDIUM POSITIONAL0.230.5
2A213LOOSE POSITIONAL0.555
2A240MEDIUM THERMAL0.732
2A213LOOSE THERMAL0.9110
3A28MEDIUM POSITIONAL0.110.5
3A23LOOSE POSITIONAL0.295
3A28MEDIUM THERMAL1.12
3A23LOOSE THERMAL1.0510
4B120MEDIUM POSITIONAL0.240.5
4B126LOOSE POSITIONAL0.485
4B1606TIGHT THERMAL1.660.5
4B120MEDIUM THERMAL2.622
4B126LOOSE THERMAL2.2710
5H68MEDIUM POSITIONAL0.160.5
5H62LOOSE POSITIONAL0.555
5H68MEDIUM THERMAL0.992
5H62LOOSE THERMAL1.0810
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 51 -
Rwork0.285 1187 -
obs--99.92 %
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)
111.75961.473-0.1681.39451.56683.53790.38190.6029-0.9821-0.1961-0.20380.1128-0.1601-0.2325-0.17810.24690.0089-0.10590.2253-0.15810.3054-61.10312.4861-22.3163
220.93543.22457.57871.36090.50133.29980.3480.4115-0.33970.09460.00840.11540.17120.1886-0.35640.2178-0.0038-0.04970.0731-0.09760.3135-25.06832.5843-12.2793
32.80820.2660.30332.6076-0.22383.28420.1168-0.23510.00230.3145-0.1217-0.112-0.03550.06940.00490.1134-0.04320.00290.0566-0.0680.19236.302312.9927.0426
415.05891.94314.12482.16532.04535.1959-0.00460.17540.0422-0.3111-0.00170.26360.1331-0.14760.00630.2071-0.0742-0.06890.0587-0.05480.2916-76.2674-33.82150.354
516.31543.9363.62683.09510.08841.5450.2024-0.26160.15830.1531-0.13430.00330.1202-0.142-0.06810.17740.0061-0.03990.1103-0.05040.1749-40.2023-31.66610.9991
63.6940.06670.06723.3340.03853.42050.0847-0.596-0.01320.3079-0.0765-0.0295-0.05190.2117-0.00810.1206-0.0955-0.01530.254-0.03060.0239-7.716-18.466626.527
714.5075-1.1293-3.48144.16112.21041.8554-0.4916-0.91820.39210.70130.39080.03820.17610.48010.10090.9166-0.3918-0.17130.5068-0.23720.740517.080424.244619.0569
81.0899-0.9603-3.90461.02313.741614.60670.1862-0.4020.3066-0.00170.4096-0.0577-0.6131.684-0.59580.6333-0.287-0.06050.7501-0.08980.69283.286-5.575735.7595
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A297 - 364
2X-RAY DIFFRACTION2A365 - 434
3X-RAY DIFFRACTION3B449 - 699
4X-RAY DIFFRACTION3A435 - 444
5X-RAY DIFFRACTION4C297 - 364
6X-RAY DIFFRACTION5C365 - 434
7X-RAY DIFFRACTION6D449 - 699
8X-RAY DIFFRACTION6C435 - 444
9X-RAY DIFFRACTION7H5 - 38
10X-RAY DIFFRACTION8I6 - 38

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