[English] 日本語
Yorodumi
- PDB-1zjk: Crystal structure of the zymogen catalytic region of human MASP-2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1zjk
TitleCrystal structure of the zymogen catalytic region of human MASP-2
ComponentsMannan-binding lectin serine protease 2
KeywordsHYDROLASE / beta barrel / modular protein
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 / calcium-dependent protein binding / peptidase activity / serine-type endopeptidase activity ...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 / calcium-dependent protein binding / peptidase activity / serine-type endopeptidase activity / calcium ion binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding
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 / Calcium-binding EGF domain / Sushi repeat (SCR repeat) ...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 / 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/SCR/CCP superfamily / Sushi/CCP/SCR domain profile. / 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 / Ribbon / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Mannan-binding lectin serine protease 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsGal, P. / Harmat, V. / Kocsis, A. / Bian, T. / Barna, L. / Ambrus, G. / Vegh, B. / Balczer, J. / Sim, R.B. / Naray-Szabo, G. / Zavodszky, P.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: A True Autoactivating Enzyme: Structural insight into mannose-binding lectin-associated serine protease-2 activations
Authors: Gal, P. / Harmat, V. / Kocsis, A. / Bian, T. / Barna, L. / Ambrus, G. / Vegh, B. / Balczer, J. / Sim, R.B. / Naray-Szabo, G. / Zavodszky, P.
#1: Journal: J.Mol.Biol. / Year: 2004
Title: The Structure of MBL-Associated Serine Protease-2 Reveals that Identical Substrate Specificities of C1s and MASP-2 are Realized Through Different Sets of Enzyme-Substrate Interactions
Authors: Harmat, V. / Gal, P. / Kardos, J. / Szilagyi, K. / Ambrus, G. / Vegh, B. / Naray-Szabo, G. / Zavodszky, P.
History
DepositionApr 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mannan-binding lectin serine protease 2


Theoretical massNumber of molelcules
Total (without water)44,0321
Polymers44,0321
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.665, 72.689, 110.989
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Mannan-binding lectin serine protease 2 / Mannose-binding protein associated serine protease 2 / MASP-2 / MBL- associated serine protease 2


Mass: 44031.715 Da / Num. of mol.: 1
Fragment: complement control protein modules 1,2 and serine protease domain
Mutation: R444Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MASP2 / Plasmid: pET-17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O00187, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 6000, sodium chloride, TRIS/HCl buffer, pH 8.0, temperature 293K, VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9392 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 18, 2003 / Details: toroidal focusing mirror
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9392 Å / Relative weight: 1
ReflectionResolution: 2.18→28.9 Å / Num. all: 18330 / Num. obs: 18330 / % possible obs: 88.1 % / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 15.13
Reflection shellResolution: 2.18→2.25 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 1.9 / Num. unique all: 800 / % possible all: 43.1

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SP domain of PDB ENTRY 1Q3X

1q3x


Resolution: 2.18→28.9 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.908 / SU B: 8.011 / SU ML: 0.194 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.352 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25285 938 5.1 %RANDOM
Rwork0.20491 ---
all0.20733 17391 --
obs0.20733 17391 88.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.915 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2---2.56 Å20 Å2
3---2.83 Å2
Refinement stepCycle: LAST / Resolution: 2.18→28.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2909 0 0 84 2993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0212996
X-RAY DIFFRACTIONr_bond_other_d0.0010.022605
X-RAY DIFFRACTIONr_angle_refined_deg0.8751.9444091
X-RAY DIFFRACTIONr_angle_other_deg0.63936045
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.195388
X-RAY DIFFRACTIONr_chiral_restr0.0560.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023408
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02610
X-RAY DIFFRACTIONr_nbd_refined0.2010.3717
X-RAY DIFFRACTIONr_nbd_other0.2390.32956
X-RAY DIFFRACTIONr_nbtor_other0.1190.52061
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2280.5130
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.324
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2690.372
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.513
X-RAY DIFFRACTIONr_mcbond_it1.2921924
X-RAY DIFFRACTIONr_mcangle_it2.13533075
X-RAY DIFFRACTIONr_scbond_it0.98821072
X-RAY DIFFRACTIONr_scangle_it1.49131016
LS refinement shellResolution: 2.18→2.237 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.346 27
Rwork0.309 615
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)
18.1843-7.5141-2.461319.70676.71545.04780.19420.31190.5193-0.5264-0.57680.9744-0.5584-0.51780.38260.24010.1266-0.02940.2142-0.0380.2412-31.43346.50952.769
24.8401-3.0045-0.96036.27611.84491.9652-0.02310.05060.00470.1939-0.1193-0.12150.1490.11710.14240.24530.03450.04360.23320.02430.0157-11.1317.23348.055
33.94990.3759-1.11983.30760.4012.7452-0.14790.01680.05060.11780.2136-0.29280.13350.1127-0.06580.08520.0441-0.04090.1179-0.03250.067914.4272.94627.462
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA296 - 36513 - 82
2X-RAY DIFFRACTION2AA366 - 43383 - 150
3X-RAY DIFFRACTION3AA434 - 686151 - 403

+
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