[English] 日本語
Yorodumi
- PDB-5cis: The CUB1-EGF-CUB2 domains of rat MBL-associated serine protease-2... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cis
TitleThe CUB1-EGF-CUB2 domains of rat MBL-associated serine protease-2 (MASP-2) bound to Ca2+
ComponentsMannan-binding lectin serine peptidase 2
KeywordsHYDROLASE / MASP / CUB1-EGF-CUB2 / Complement activation / lectin pathway
Function / homology
Function and homology information


Ficolins bind to repetitive carbohydrate structures on the target cell surface / mannan-binding lectin-associated serine protease-2 / complement component C4b binding / Lectin pathway of complement activation / positive regulation of opsonization / complement activation, lectin pathway / cell surface pattern recognition receptor signaling pathway / serine-type endopeptidase complex / symbiont cell surface / complement activation ...Ficolins bind to repetitive carbohydrate structures on the target cell surface / mannan-binding lectin-associated serine protease-2 / complement component C4b binding / Lectin pathway of complement activation / positive regulation of opsonization / complement activation, lectin pathway / cell surface pattern recognition receptor signaling pathway / serine-type endopeptidase complex / symbiont cell surface / complement activation / zymogen activation / complement activation, classical pathway / protein maturation / calcium-dependent protein binding / peptidase activity / serine-type endopeptidase activity / calcium ion binding / Golgi apparatus / cell surface / proteolysis / : / extracellular region / identical protein binding
Similarity search - Function
Spermadhesin, CUB domain / Peptidase S1A, complement C1r/C1S/mannan-binding / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / Spermadhesin, CUB domain superfamily / CUB domain profile. / : / Calcium-binding EGF domain / Sushi repeat (SCR repeat) ...Spermadhesin, CUB domain / Peptidase S1A, complement C1r/C1S/mannan-binding / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / Spermadhesin, CUB domain superfamily / CUB domain profile. / : / 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 / Laminin / Laminin / 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 / Serine proteases, trypsin family, serine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Jelly Rolls / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Sandwich / Mainly Beta
Similarity search - Domain/homology
Mannan-binding lectin serine protease 2 / Mannan-binding lectin serine protease 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.58 Å
AuthorsNan, R. / Furze, C.M. / Wright, D.W. / Gor, J. / Wallis, R. / Perkins, S.J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/K011715/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/K039121/1 United Kingdom
CitationJournal: Structure / Year: 2017
Title: Flexibility in Mannan-Binding Lectin-Associated Serine Proteases-1 and -2 Provides Insight on Lectin Pathway Activation.
Authors: Nan, R. / Furze, C.M. / Wright, D.W. / Gor, J. / Wallis, R. / Perkins, S.J.
History
DepositionJul 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Feb 15, 2017Group: Database references
Revision 1.3Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_data_processing_status ...diffrn_source / pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.7Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.8Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.9Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mannan-binding lectin serine peptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8685
Polymers31,5271
Non-polymers3414
Water1,60389
1
A: Mannan-binding lectin serine peptidase 2
hetero molecules

A: Mannan-binding lectin serine peptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,73710
Polymers63,0542
Non-polymers6838
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2900 Å2
ΔGint-33 kcal/mol
Surface area29990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.930, 98.300, 121.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Mannan-binding lectin serine peptidase 2 / Mannan-binding lectin serine peptidase 2 / isoform CRA_b / Mannan-binding lectin serine protease 2


Mass: 31526.973 Da / Num. of mol.: 1 / Fragment: UNP residues 21-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Masp2, rCG_31002 / Plasmid: PED / Cell (production host): OVARY / Cell line (production host): DXB11 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: A2VCV7, UniProt: Q9JJS8*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris pH 8.5 containing 80 mM ammonium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.58→50.3 Å / Num. obs: 12626 / % possible obs: 97.6 % / Redundancy: 3.9 % / Rsym value: 0.099 / Net I/σ(I): 11.58
Reflection shellResolution: 2.58→2.6 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 2.03 / % possible all: 93.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NTO

1nto


Resolution: 2.58→50.343 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2407 585 4.64 %Random selection
Rwork0.2003 12035 --
obs0.2022 12620 97.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 209.1 Å2 / Biso mean: 54.0467 Å2 / Biso min: 24.13 Å2
Refinement stepCycle: final / Resolution: 2.58→50.343 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2208 0 17 89 2314
Biso mean--80.96 46.94 -
Num. residues----276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032298
X-RAY DIFFRACTIONf_angle_d0.7123117
X-RAY DIFFRACTIONf_chiral_restr0.028325
X-RAY DIFFRACTIONf_plane_restr0.003407
X-RAY DIFFRACTIONf_dihedral_angle_d11.066823
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.58-2.83960.33081270.28712923305096
2.8396-3.25050.31211530.253007316099
3.2505-4.0950.23131500.19242989313997
4.095-50.35290.2011550.16593116327198
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)
13.29810.98260.27396.6442-0.12273.0434-0.1144-0.00990.47440.14320.05070.071-0.27710.06520.03890.23440.0142-0.01810.34430.00030.2665-27.291723.57820.9703
20.201-0.99161.04327.6381-6.84916.50140.0954-0.15950.18430.6695-0.2451-0.402-0.41980.38060.14690.3544-0.0101-0.00550.4807-0.02320.3034-27.8973-4.440211.6978
34.6805-1.30920.83227.1473-2.4476.7917-0.08360.0145-0.02610.1610.1324-0.16230.1902-0.0182-0.10740.26-0.0008-0.01070.3736-0.02640.2658-20.6165-25.816139.2426
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 109 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 110 through 160 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 161 through 279 )A0

+
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