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- PDB-4iw4: Crystal structure of the serine protease domain of MASP-3 in comp... -

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Basic information

Entry
Database: PDB / ID: 4iw4
TitleCrystal structure of the serine protease domain of MASP-3 in complex with ecotin
Components
  • Ecotin
  • Mannan-binding lectin serine protease 3
KeywordsHYDROLASE/HYDROLASE INHIBITOR / trypsin-like fold / protease / inhibitor / extracellular / 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 / zymogen activation / 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 ...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 / zymogen activation / 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 / 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 / extracellular space / extracellular region / nucleoplasm / identical protein binding / cytosol
Similarity search - Function
Ecotin / 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 ...Ecotin / 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 / 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / 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 / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ecotin / Mannan-binding lectin serine protease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsGaboriaud, C.
CitationJournal: Plos One / Year: 2013
Title: The Serine Protease Domain of MASP-3: Enzymatic Properties and Crystal Structure in Complex with Ecotin.
Authors: Gaboriaud, C. / Gupta, R.K. / Martin, L. / Lacroix, M. / Serre, L. / Teillet, F. / Arlaud, G.J. / Rossi, V. / Thielens, N.M.
History
DepositionJan 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Ecotin
D: Ecotin
E: Mannan-binding lectin serine protease 3
F: Mannan-binding lectin serine protease 3


Theoretical massNumber of molelcules
Total (without water)93,4104
Polymers93,4104
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10630 Å2
ΔGint-44 kcal/mol
Surface area30760 Å2
MethodPISA
2
C: Ecotin
D: Ecotin
E: Mannan-binding lectin serine protease 3
F: Mannan-binding lectin serine protease 3

C: Ecotin
D: Ecotin
E: Mannan-binding lectin serine protease 3
F: Mannan-binding lectin serine protease 3


Theoretical massNumber of molelcules
Total (without water)186,8208
Polymers186,8208
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area24100 Å2
ΔGint-104 kcal/mol
Surface area58680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.720, 164.620, 90.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.998784, 0.008141, -0.048623), (0.008287, -0.944513, -0.32837), (-0.048598, -0.328374, 0.943297)-12.35678, 80.81499, 13.25709

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Components

#1: Protein Ecotin


Mass: 16120.507 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P23827
#2: Protein Mannan-binding lectin serine protease 3


Mass: 30584.471 Da / Num. of mol.: 2 / Fragment: serine protease domain (UNP residues 450-728)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Hi-5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P48740
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DEPOSITED SEQUENCE CORRESPONDS TO ISOFORM 2 OF UNP ENTRY P48740

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 20% PEG2000MME, 0.2M ammonium sulfate, 0.1M sodium acetate pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-110.9334
SYNCHROTRONESRF ID14-220.933
SYNCHROTRONESRF ID2930.97618
SYNCHROTRONESRF BM1440.97624
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDOct 4, 2009
ADSC QUANTUM 42CCDJul 2, 2009
ADSC QUANTUM 3153CCDMar 12, 2009
MARMOSAIC 225 mm CCD4CCDApr 28, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
3SINGLE WAVELENGTHMx-ray3
4SINGLE WAVELENGTHMx-ray4
Radiation wavelength
IDWavelength (Å)Relative weight
10.93341
20.9331
30.976181
40.976241
ReflectionResolution: 3.2→20 Å / Num. all: 17133 / Num. obs: 16636 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell
Resolution (Å)Diffraction-ID% possible all
3.2-3.251,2,3,490.4
10-201,2,3,498.4
6-101,2,3,499.5
4-61,2,3,499.2
3.5-41,2,3,496.5
3.25-3.31,2,3,492.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→19.98 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.875 / SU B: 54.361 / SU ML: 0.414 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.522 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26908 852 5 %RANDOM
Rwork0.20778 ---
obs0.21094 16187 99.45 %-
all-16276 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.479 Å2
Baniso -1Baniso -2Baniso -3
1--4.19 Å20 Å20 Å2
2---2.49 Å20 Å2
3---6.68 Å2
Refinement stepCycle: LAST / Resolution: 3.2→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5731 0 0 4 5735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195880
X-RAY DIFFRACTIONr_bond_other_d0.0020.025463
X-RAY DIFFRACTIONr_angle_refined_deg1.1281.9548034
X-RAY DIFFRACTIONr_angle_other_deg0.7493.00212516
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.675742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55524.383235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.99115873
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.61521
X-RAY DIFFRACTIONr_chiral_restr0.0120.2905
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216666
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021307
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
LS refinement shellResolution: 3.2→3.281 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 60 -
Rwork0.259 1152 -
obs--100 %
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)
11.85091.0610.45394.99130.16420.84940.13210.1291-0.40270.41420.0153-0.78330.19380.0512-0.14730.37070.0387-0.0750.28080.12690.24464.58838.186-15.846
20.41610.901-0.13175.61250.91620.81520.0618-0.19710.12820.2642-0.27790.98860.1134-0.15090.21620.2998-0.05770.15060.32050.0210.3075-15.58950.462-14.441
32.9086-0.365-0.10444.24420.14022.66010.0709-0.0263-0.18330.11160.0384-0.61910.19640.1141-0.10930.11610.0102-0.02780.11650.04780.166111.91469.469-19.934
43.2334-0.09380.25793.95270.52363.29130.1765-0.015-0.16310.029-0.15150.88880.0794-0.2174-0.02510.3872-0.1095-0.03420.15940.01550.4432-23.44822.348-28.598
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C5 - 142
2X-RAY DIFFRACTION2D6 - 142
3X-RAY DIFFRACTION3E431 - 704
4X-RAY DIFFRACTION4F431 - 697

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