[English] 日本語
Yorodumi
- PDB-3gov: Crystal structure of the catalytic region of human MASP-1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gov
TitleCrystal structure of the catalytic region of human MASP-1
Components(MASP-1) x 2
KeywordsHYDROLASE / Complement / serine protease / beta barrel / Hydroxylation / Immune response / Innate immunity / Sushi / Coagulation / Complement pathway / Disulfide bond / EGF-like domain / Glycoprotein / Protease
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 / 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 / zymogen activation / 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 / extracellular space / extracellular region / nucleoplasm / identical protein binding / cytosol
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 / 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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
Mannan-binding lectin serine protease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsHarmat, V. / Dobo, J. / Beinrohr, L. / Sebestyen, E. / Zavodszky, P. / Gal, P.
CitationJournal: J.Immunol. / Year: 2009
Title: MASP-1, a promiscuous complement protease: structure of its catalytic region reveals the basis of its broad specificity.
Authors: Dobo, J. / Harmat, V. / Beinrohr, L. / Sebestyen, E. / Zavodszky, P. / Gal, P.
History
DepositionMar 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 25, 2013Group: Derived calculations
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MASP-1
B: MASP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7214
Polymers45,5372
Non-polymers1842
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-13 kcal/mol
Surface area20110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.418, 70.412, 121.413
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 17508.240 Da / Num. of mol.: 1
Fragment: Sushi-1 and Sushi-2 domains, CCP1-CCP2, 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: Protein MASP-1 / Ra-reactive factor serine protease p100 / RaRF / Mannan-binding lectin serine protease 1 / Mannose- ...Ra-reactive factor serine protease p100 / RaRF / Mannan-binding lectin serine protease 1 / Mannose-binding protein-associated serine protease / MASP-1 / Serine protease 5 / Complement-activating component of Ra-reactive factor heavy chain / Complement-activating component of Ra-reactive factor light chain


Mass: 28028.900 Da / Num. of mol.: 1 / Fragment: serine protease 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAINS A AND B ARE PRODUCTS OF SPECIFIC CLEAVAGE OF THE ARG448-ILE449 BOND DURING SPONTANEOUS ...CHAINS A AND B ARE PRODUCTS OF SPECIFIC CLEAVAGE OF THE ARG448-ILE449 BOND DURING SPONTANEOUS AUTOACTIVATION OF MASP-1
Sequence detailsTHE RESIDUE AT POSITION 499 IS A NATURAL VARIANT OF THE ENZYME

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: well solution: 11%(w/v) PEG3350, 0.1 M MES; protein solution: 50 mM NaCl, 5 mM Tris, 0.5 mM EDTA, 20 mM benzamidine-HCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8148 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 1, 2007 / Details: mirrors
RadiationMonochromator: Si [111], horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8148 Å / Relative weight: 1
ReflectionResolution: 2.55→45.98 Å / Num. obs: 19349 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 30.892 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 15.96
Reflection shellResolution: 2.55→2.6 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 4.3 / Num. measured obs: 6216 / Num. unique all: 1066 / Num. unique obs: 1066 / % possible all: 97.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MASP-1 serine protease domain(unpublished), CCP1 and CCP2 modules of PDB entry 1zjk

1zjk


Resolution: 2.55→45.98 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.859 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 24.172 / SU ML: 0.252 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.453 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.278 989 5.1 %RANDOM
Rwork0.229 ---
all0.231 ---
obs0.231 19342 97.92 %-
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 max: 65.76 Å2 / Biso mean: 48.887 Å2 / Biso min: 23.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2--0.19 Å20 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 2.55→45.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3065 0 12 90 3167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223196
X-RAY DIFFRACTIONr_bond_other_d0.0020.022174
X-RAY DIFFRACTIONr_angle_refined_deg1.1631.9594352
X-RAY DIFFRACTIONr_angle_other_deg0.8243.0065319
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4195406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27824.887133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92915529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5821511
X-RAY DIFFRACTIONr_chiral_restr0.0710.2472
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023546
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02600
X-RAY DIFFRACTIONr_nbd_refined0.190.2543
X-RAY DIFFRACTIONr_nbd_other0.1880.22115
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21477
X-RAY DIFFRACTIONr_nbtor_other0.0810.21701
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2103
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0970.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1570.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0820.26
X-RAY DIFFRACTIONr_mcbond_it0.62322057
X-RAY DIFFRACTIONr_mcbond_other0.0962810
X-RAY DIFFRACTIONr_mcangle_it1.04633230
X-RAY DIFFRACTIONr_scbond_it0.42921319
X-RAY DIFFRACTIONr_scangle_it0.67431117
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 78 -
Rwork0.337 1318 -
all-1396 -
obs-1438 97.08 %
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)
10.7489-1.2185-0.32312.04723.17691.2885-0.0639-0.07210.04010.34080.2322-0.55490.10620.0449-0.1683-0.20630.00410.0003-0.10740.0042-0.169.953541.585825.6109
22.4316-0.47951.57991.5227-0.21064.20390.01010.2328-0.24-0.1640.0511-0.0310.25730.2418-0.0612-0.1533-0.01120.0252-0.1738-0.0149-0.1291-0.6742-8.14832.0919
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A298 - 435
2X-RAY DIFFRACTION2A436 - 699

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more