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- PDB-7arx: Crystal structure of the catalytic fragment of masp-1 in complex ... -

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Basic information

Entry
Database: PDB / ID: 7arx
TitleCrystal structure of the catalytic fragment of masp-1 in complex with SFMI1
Components
  • (Mannan-binding lectin serine protease 1) x 2
  • SFMI1 - Sunflower MASP1 inhibitor
KeywordsIMMUNE SYSTEM / protease / 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 / calcium-dependent protein binding / peptidase activity / serine-type endopeptidase 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 / 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
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 / 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. ...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 / 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 / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Mannan-binding lectin serine protease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Helianthus annuus (common sunflower)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsDurvanger, Z. / Harmat, V. / Dobo, J. / Megyeri, M.
Funding support Hungary, 3items
OrganizationGrant numberCountry
European Regional Development FundVEKOP-2.3.3-15-2017-00020, VEKOP-2.3.2-16-2017-00014 and VEKOP-2.3.3-15-2017-00018 Hungary
Hungarian National Research, Development and Innovation Office2018-1.2.1-NKP-2018-00005 Hungary
Hungarian National Research, Development and Innovation OfficeNK100769, NK100834, K116305, K119374 and K119386 Hungary
Citation
Journal: Acs Chem.Biol. / Year: 2022
Title: Directed Evolution-Driven Increase of Structural Plasticity Is a Prerequisite for Binding the Complement Lectin Pathway Blocking MASP-Inhibitor Peptides.
Authors: Durvanger, Z. / Boros, E. / Nagy, Z.A. / Hegedus, R. / Megyeri, M. / Dobo, J. / Gal, P. / Schlosser, G. / Angyan, A.F. / Gaspari, Z. / Perczel, A. / Harmat, V. / Mezo, G. / Menyhard, D.K. / Pal, G.
#1: Journal: J Immunol. / Year: 2010
Title: Selective inhibition of the lectin pathway of complement with phage display selected peptides against mannose-binding lectin-associated serine protease (MASP)-1 and -2: significant ...Title: Selective inhibition of the lectin pathway of complement with phage display selected peptides against mannose-binding lectin-associated serine protease (MASP)-1 and -2: significant contribution of MASP-1 to lectin pathway activation.
Authors: Kocsis, A. / Kekesi, K.A. / Szasz, R. / Vegh, B.M. / Balczer, J. / Dobo, J. / Zavodszky, P. / Gal, P. / Pal, G.
History
DepositionOct 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 2.0Feb 23, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_name_com / entity_src_gen / pdbx_contact_author / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.beg_label_asym_id / _pdbx_refine_tls_group.beg_label_seq_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_refine_tls_group.end_label_asym_id / _pdbx_refine_tls_group.end_label_seq_id / _pdbx_refine_tls_group.selection_details / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _software.name / _software.version / _struct_conn.pdbx_dist_value / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Description: Model completeness
Details: During the review of our manuscript a referee suggested that atom O of Cys11 (chain C) was in place of a nitrogen from Ile12. Backbone atoms of Ile12 was built in the model to correct this error.
Provider: author / Type: Coordinate replacement
Revision 2.1May 18, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 2.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
B: Mannan-binding lectin serine protease 1
C: SFMI1 - Sunflower MASP1 inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1154
Polymers47,0093
Non-polymers1061
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Complement deposition ELISA assays, in vitro inhibition assay
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-13 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.300, 69.300, 161.800
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Mannan-binding lectin serine protease 1 / Complement factor MASP-3 / Complement-activating component of Ra-reactive factor / Mannose-binding ...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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MASP1, CRARF, CRARF1, PRSS5 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P48740, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein Mannan-binding lectin serine protease 1 / Complement factor MASP-3 / Complement-activating component of Ra-reactive factor / Mannose-binding ...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: 28028.834 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MASP1, CRARF, CRARF1, PRSS5 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P48740, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#3: Protein/peptide SFMI1 - Sunflower MASP1 inhibitor


Mass: 1471.765 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Peptide was developed by phage display technique based on the SFTI inhibitor (UniProt ID Q4GWU5) to selectively inhibit MASP-1
Source: (synth.) Helianthus annuus (common sunflower)
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.39 Å3/Da / Density % sol: 48.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Hepes, 42 w/v% PEG200, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.9769 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9769 Å / Relative weight: 1
ReflectionResolution: 2.42→29.52 Å / Num. obs: 17832 / % possible obs: 97.1 % / Redundancy: 7.83 % / Biso Wilson estimate: 64.31 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.106 / Net I/σ(I): 14.74
Reflection shellResolution: 2.42→2.5 Å / Redundancy: 7.05 % / Num. unique obs: 1564 / CC1/2: 0.314 / Rrim(I) all: 2.08 / % possible all: 76.7

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GOV

3gov


Resolution: 2.42→19.85 Å / SU ML: 0.4648 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.8287
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2849 855 4.94 %
Rwork0.256 16446 -
obs0.2574 17301 96.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.57 Å2
Refinement stepCycle: LAST / Resolution: 2.42→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2944 0 7 26 2977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00163025
X-RAY DIFFRACTIONf_angle_d0.45244139
X-RAY DIFFRACTIONf_chiral_restr0.0418467
X-RAY DIFFRACTIONf_plane_restr0.0035542
X-RAY DIFFRACTIONf_dihedral_angle_d9.77851015
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.570.3951180.38522296X-RAY DIFFRACTION82.28
2.57-2.770.40681510.36642724X-RAY DIFFRACTION98.46
2.77-3.040.38491410.34392776X-RAY DIFFRACTION99.9
3.05-3.480.31951440.27642816X-RAY DIFFRACTION100
3.48-4.380.24821520.22692851X-RAY DIFFRACTION100
4.38-19.850.25051490.22512983X-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)
11.179420461110.0174244888751-0.1521202274151.001882201530.354932118594-0.6548765458050.0307110949186-0.186865417566-0.281698847228-0.106671094648-0.292337753536-0.447242437178-0.0839718708282-0.0154502334375-1.73666305892E-50.782512254383-0.1406280125810.08570774768180.6512710501060.01502615443660.81850562954212.4498688843-76.096597205519.3081478858
23.07723391428-0.8757068527590.8065533625582.569599108310.854304041473.239398988510.1745488067140.05159991296790.289590323291-0.363456790483-0.257951159183-0.228026935713-0.585666999352-0.5553646145152.28904270703E-50.8544191023880.0826128915830.08629100276680.6558681734760.072134657640.62668556195917.3020012415-9.759675706159.24716507039
31.713226972132.118551307911.157017444492.606114770511.438987805430.7804261038280.3382114932990.1374147220611.01419473005-1.2311929693-0.6014931273290.852568039477-1.7148238977-1.17157475186-0.1363957099721.449762445570.5752092251240.07913397241060.9020498095080.05363148489240.54404304851215.67385061841.40303275050.446820440379
40.0575336781647-0.0585841636718-0.3599090946220.830547242336-0.1262143355281.13533228427-0.251521396501-0.139653405576-0.14239444021-0.4096058734660.157333338686-0.1962916231390.0563857716646-0.1947258290042.43446059236E-60.732060034545-0.07724299253620.02347153172730.6207193878120.03262331664570.81302955882118.9895160145-40.252690370921.6658668668
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and resseq 295:382
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'A' and resseq 385:445

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