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- PDB-7pqn: Catalytic fragment of MASP-2 in complex with ecotin -

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Basic information

Entry
Database: PDB / ID: 7pqn
TitleCatalytic fragment of MASP-2 in complex with ecotin
Components
  • Ecotin
  • Mannan-binding lectin serine protease 2 A chain
  • Mannan-binding lectin serine protease 2 B chain
KeywordsIMMUNE SYSTEM / serine protease / complement / inhibitor
Function / homology
Function and homology information


mannan-binding lectin-associated serine protease-2 / complement component C4b binding / Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / complement activation, lectin pathway / Initial triggering of complement / complement activation, classical pathway / serine-type endopeptidase inhibitor activity / defense response / calcium-dependent protein binding ...mannan-binding lectin-associated serine protease-2 / complement component C4b binding / Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / complement activation, lectin pathway / Initial triggering of complement / complement activation, classical pathway / serine-type endopeptidase inhibitor activity / defense response / calcium-dependent protein binding / peptidase activity / outer membrane-bounded periplasmic space / serine-type endopeptidase activity / calcium ion binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Ecotin, C-terminal / Proteinase inhibitor I11, ecotin / Proteinase inhibitor I11, ecotin, gammaproteobacteria / Ecotin superfamily / Ecotin / 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. ...Ecotin, C-terminal / Proteinase inhibitor I11, ecotin / Proteinase inhibitor I11, ecotin, gammaproteobacteria / Ecotin superfamily / Ecotin / 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 / : / Calcium-binding EGF domain / 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-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 / 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
Mannan-binding lectin serine protease 2 / Ecotin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.40001520992 Å
AuthorsHarmat, V. / Fodor, K. / Heja, D.
Funding support Hungary, 6items
OrganizationGrant numberCountry
Ministry of Human Capacities2018-1.2.1-NKP-2018-00005 Hungary
National Research Development and Innovation Office (NKFIH)OTKA K 119386 Hungary
National Research Development and Innovation Office (NKFIH)OTKA K 119374 Hungary
National Research Development and Innovation Office (NKFIH)OTKA K 135289 Hungary
European Regional Development FundVEKOP-2.3.3-15-2017-00018 Hungary
European Regional Development FundVEKOP-2.3.2-16-2017-00014 Hungary
Citation
Journal: J.Biol.Chem. / Year: 2022
Title: Synergy of protease-binding sites within the ecotin homodimer is crucial for inhibition of MASP enzymes and for blocking lectin pathway activation.
Authors: Nagy, Z.A. / Heja, D. / Bencze, D. / Kiss, B. / Boros, E. / Szakacs, D. / Fodor, K. / Wilmanns, M. / Kocsis, A. / Dobo, J. / Gal, P. / Harmat, V. / Pal, G.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart /
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
#3: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: XDS.
Authors: Kabsch, W.
#4: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: Molecular replacement with MOLREP.
Authors: Vagin, A. / Teplyakov, A.
#5: Journal: PLoS Pathog / Year: 2019
Title: Ecotin, a microbial inhibitor of serine proteases, blocks multiple complement dependent and independent microbicidal activities of human serum.
Authors: Nagy, Z.A. / Szakacs, D. / Boros, E. / Heja, D. / Vigh, E. / Sandor, N. / Jozsi, M. / Oroszlan, G. / Dobo, J. / Gal, P. / Pal, G.
History
DepositionSep 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
Revision 1.3Nov 20, 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
C: Ecotin
D: Ecotin
A: Mannan-binding lectin serine protease 2 A chain
B: Mannan-binding lectin serine protease 2 B chain
aa: Mannan-binding lectin serine protease 2 A chain
bb: Mannan-binding lectin serine protease 2 B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,2539
Polymers107,9776
Non-polymers2763
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12870 Å2
ΔGint-72 kcal/mol
Surface area38430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.562, 102.746, 109.938
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALPROPRO(chain 'C' and ((resid 4 through 5 and (name N...CA4 - 8824 - 108
121GLYGLYARGARG(chain 'C' and ((resid 4 through 5 and (name N...CA90 - 142110 - 162
211VALVALPROPRO(chain 'D' and (resid 4 through 7 or (resid 8...DB4 - 8824 - 108
221GLYGLYARGARG(chain 'D' and (resid 4 through 7 or (resid 8...DB90 - 142110 - 162
132ASPASPGLUGLU(chain 'A' and (resid 365 through 396 or (resid 397...AC365 - 4137 - 55
142GLYGLYTHRTHR(chain 'A' and (resid 365 through 396 or (resid 397...AC416 - 44058 - 82
152ILEILETYRTYR(chain 'A' and (resid 365 through 396 or (resid 397...BD445 - 6021 - 158
162SERSERSERSER(chain 'A' and (resid 365 through 396 or (resid 397...BD611 - 628167 - 184
172ARGARGMETMET(chain 'A' and (resid 365 through 396 or (resid 397...BD630 - 658186 - 214
182GLYGLYPHEPHE(chain 'A' and (resid 365 through 396 or (resid 397...BD661 - 686217 - 242
232ASPASPGLUGLU(chain 'B' and (resid 365 through 375 or (resid 376...aaE365 - 4137 - 55
242GLYGLYTHRTHR(chain 'B' and (resid 365 through 375 or (resid 376...aaE416 - 44058 - 82
252ILEILETYRTYR(chain 'B' and (resid 365 through 375 or (resid 376...bbF445 - 6021 - 158
262SERSERSERSER(chain 'B' and (resid 365 through 375 or (resid 376...bbF611 - 628167 - 184
272ARGARGMETMET(chain 'B' and (resid 365 through 375 or (resid 376...bbF630 - 658186 - 214
282GLYGLYPHEPHE(chain 'B' and (resid 365 through 375 or (resid 376...bbF661 - 686217 - 242

NCS ensembles :
ID
1
2

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Components

#1: Protein Ecotin


Mass: 18214.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: eco, eti, b2209, JW2197 / Production host: Escherichia coli (E. coli) / References: UniProt: P23827
#2: Protein Mannan-binding lectin serine protease 2 A chain


Mass: 9231.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ASMT expression tag is followed by residue 363 of the sequence. The enzyme is activated: the peptide bond between residues 444 and 445 is hydrolyzed.
Source: (gene. exp.) Homo sapiens (human) / Gene: MASP2 / Plasmid: pET-17B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O00187
#3: Protein Mannan-binding lectin serine protease 2 B chain


Mass: 26542.971 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ASMT expression tag is followed by residue 363 of the sequence. The enzyme is activated: the peptide bond between residues 444 and 445 is hydrolyzed.
Source: (gene. exp.) Homo sapiens (human) / Gene: MASP2 / Plasmid: pET-17B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O00187
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.6 Å3/Da / Density % sol: 52.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 17% (w/v) PEG 3350, 0.3M LiCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97942 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 44699 / % possible obs: 99.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 48.3960860041 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.094 / Net I/σ(I): 13.5
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3.52 % / Num. unique obs: 5067 / CC1/2: 0.994 / Rrim(I) all: 0.755 / % possible all: 75.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB structure 1AZZ and SP and CCP2 domains from pdb structure 1Q3X.

1azz

1q3x


Resolution: 2.40001520992→29.8335295021 Å / SU ML: 0.3624288238 / Cross valid method: FREE R-VALUE / σ(F): 1.35511395054 / Phase error: 26.3346467713
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.232889785295 2217 4.96806722689 %
Rwork0.192094143757 42408 -
obs0.194207570392 44625 99.7139856546 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.9461290296 Å2
Refinement stepCycle: LAST / Resolution: 2.40001520992→29.8335295021 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6742 0 18 116 6876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006747857286546942
X-RAY DIFFRACTIONf_angle_d0.8827534748819492
X-RAY DIFFRACTIONf_chiral_restr0.05436493983921071
X-RAY DIFFRACTIONf_plane_restr0.005884258541011219
X-RAY DIFFRACTIONf_dihedral_angle_d9.967435988044069
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.40001520992-2.45220.3367205416061340.2985595378882595X-RAY DIFFRACTION99.1282237559
2.4522-2.50920.3165994904221320.2821959773792639X-RAY DIFFRACTION99.1768074445
2.5092-2.57190.3604615291651370.2753987577182572X-RAY DIFFRACTION99.2671308171
2.5719-2.64140.3065903757131340.2730362280972626X-RAY DIFFRACTION99.8191681736
2.6414-2.71910.3086637116561340.2700636567052608X-RAY DIFFRACTION99.9635435654
2.7191-2.80680.3097986578221430.2558011582992628X-RAY DIFFRACTION99.9278759466
2.8068-2.9070.3313088664341360.2518097229882634X-RAY DIFFRACTION100
2.907-3.02330.2639797708031400.2357972721692641X-RAY DIFFRACTION99.928135106
3.0233-3.16080.2974707384281400.2215360750282646X-RAY DIFFRACTION99.9641191245
3.1608-3.32720.287941264761360.2159334304352648X-RAY DIFFRACTION99.856527977
3.3272-3.53530.2398182657591380.1960303428982632X-RAY DIFFRACTION99.9639119451
3.5353-3.80780.2355311144311390.1671800904082659X-RAY DIFFRACTION99.8928953945
3.8078-4.19010.1924549344881420.1507871857222666X-RAY DIFFRACTION99.8932764141
4.1901-4.79420.1593892342291430.1339944398722690X-RAY DIFFRACTION99.7886579782
4.7942-6.0320.1782608651421440.1645136889872704X-RAY DIFFRACTION99.6501049685
6.032-29.83352950210.2080982010191450.1793101208932820X-RAY DIFFRACTION99.2302543507
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)
10.4475476913960.0219532982677-1.036992183920.4095550582630.617927713193.46619544696-0.133306160798-0.132608134771-0.006279731139930.114117796830.1081110096760.06877320687140.06869915001050.243872620931-0.0178975858630.4553106617560.0863475365945-0.04698751265370.460811141648-0.05314428157220.4857626979598.621745169554.9768521683220.8182934789
20.4328118135070.000132213848129-0.8361607035830.3951832434310.2611989029361.793619966490.1810728846050.1684884789210.130891010352-0.127702445597-0.160799914976-0.0347298907735-0.504749641285-0.393355167444-0.03684866926140.6681268434150.215341860048-0.006158997927520.4884813786590.01906156177360.46994111261-4.5730120800519.00072717867.03529318212
32.22904261069-1.185134842561.522510168421.90345576943-0.853923407484.1201877421-0.2485087292710.5491632020720.4775927176560.162856084709-0.0745871204608-0.0414084236035-0.390175868626-0.2834533776250.2335146294820.6030698308920.06822181940290.01167857765551.036096677290.2278916624320.6338539114476.953941243176.48255260555-44.301934666
42.23608263676-0.729009410175-0.6177225184632.2511570405-0.4178113761662.806041317130.004448316681370.1364079482710.0329573030346-0.02314210168160.01084598005740.116656008406-0.0730935824566-0.146038301005-0.01197056766070.3256386921050.02952346185550.0085202516770.3730117558820.02634733486140.3737392916212.636374396-7.05133050967-11.0214444162
52.91387482171-0.7032706265021.414437947213.14651989395-1.307254970556.68258361339-0.220925522844-1.015219744310.03918015808480.931832478799-0.175739610202-0.0467147514676-0.5534840395910.1510967155260.257454485440.743633570566-0.07691011106920.06628755894880.7490033661660.09619547932920.681293293847-17.474233252311.24156231172.4761922197
61.73511400426-0.575068515644-0.5893273063222.567035509330.5754609457093.041100161720.1891203646690.249644008523-0.264572244724-0.465436968539-0.188493714980.518438865547-0.00994165759912-0.325329334086-0.0006840331198150.4048035013750.0239964913515-0.09818834486130.381571194218-0.09131648289110.503586129418-22.176495768916.346887925336.4040867443
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 2 through 142 )
2X-RAY DIFFRACTION2chain 'D' and (resid 4 through 142 )
3X-RAY DIFFRACTION3chain 'A' and (resid 363 through 433 )
4X-RAY DIFFRACTION4chain 'B' and (resid 434 through 686 )
5X-RAY DIFFRACTION5chain 'aa' and (resid 365 through 433 )
6X-RAY DIFFRACTION6chain 'bb' and (resid 434 through 686 )

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