[English] 日本語
Yorodumi
- PDB-6ryn: Structure of conglutinin carbohydrate recognition domain with Glc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ryn
TitleStructure of conglutinin carbohydrate recognition domain with GlcNAc-alpha-1-phosphate bound
ComponentsConglutinin
KeywordsIMMUNE SYSTEM / carbohydrate recognition domain / lectin / collectin / sugar binding protein
Function / homology
Function and homology information


extracellular matrix structural constituent conferring tensile strength / collagen trimer / D-mannose binding / extracellular matrix organization / collagen-containing extracellular matrix / extracellular space
Similarity search - Function
Lung surfactant protein D coiled-coil trimerisation / Lung surfactant protein D coiled-coil trimerisation / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. ...Lung surfactant protein D coiled-coil trimerisation / Lung surfactant protein D coiled-coil trimerisation / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-GN1 / Conglutinin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsShrive, A.K. / Greenhough, T.J.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Atomic-resolution crystal structures of the immune protein conglutinin from cow reveal specific interactions of its binding site withN-acetylglucosamine.
Authors: Paterson, J.M. / Shaw, A.J. / Burns, I. / Dodds, A.W. / Prasad, A. / Reid, K.B. / Greenhough, T.J. / Shrive, A.K.
History
DepositionJun 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Conglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4644
Polymers14,0831
Non-polymers3813
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: From known literature, active molecule is composed of four trimeric units - trimeric unit is composed of N-terminal domain, collagen-like helix, alpha-helical coiled-coil and 3 carbohydrate ...Evidence: From known literature, active molecule is composed of four trimeric units - trimeric unit is composed of N-terminal domain, collagen-like helix, alpha-helical coiled-coil and 3 carbohydrate recognition domains. As the structure only contains a carbohydrate recognition domain, it is only a monomer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-23 kcal/mol
Surface area6330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.278, 50.278, 52.192
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

-
Components

#1: Protein Conglutinin /


Mass: 14082.562 Da / Num. of mol.: 1 / Fragment: carbohydrate recognition domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: CGN1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P23805
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-GN1 / 2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose / 2-(ACETYLAMINO)-2-DEOXY-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE / N-ACETYL-D-GLUCOSAMINE-1-PHOSPHATE / N-acetyl-1-O-phosphono-alpha-D-glucosamine / 2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucose / 2-acetamido-2-deoxy-1-O-phosphono-D-glucose / 2-acetamido-2-deoxy-1-O-phosphono-glucose


Type: D-saccharide / Mass: 301.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H16NO9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Glcp1PO3NAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.48 % / Mosaicity: 0.33 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 2.5 M ammonium sulfate, 0.1 M tris

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.827 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 13, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.827 Å / Relative weight: 1
ReflectionResolution: 1→50.304 Å / Num. obs: 70085 / % possible obs: 99.7 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.04 / Rrim(I) all: 0.047 / Rsym value: 0.04 / Net I/av σ(I): 9.5 / Net I/σ(I): 20.7 / Num. measured all: 538352
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRrim(I) allRsym valueNet I/σ(I) obs% possible all
1-17.40.389272439850.4630.3893.699.9
1-1.087.40.233.4104953141970.2750.236.199.9
1.08-1.197.40.1136.697105131430.1360.11312100
1.19-1.337.30.077986579118680.0940.07717.5100
1.33-1.537.40.05511.577581104860.0670.05523.8100
1.53-1.8870.04512.66253288840.0560.04530.3100
1.88-2.6690.03715.96219268860.0430.03741.699.9
2.66-52.276110.0321.14016736360.0340.0352.294.9

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.1.4data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 6RYJ

6ryj


Resolution: 1→50 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.413 / SU ML: 0.01 / SU R Cruickshank DPI: 0.0177 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.018 / ESU R Free: 0.018
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.14 3523 5 %RANDOM
Rwork0.1239 ---
obs0.1247 66521 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 81.92 Å2 / Biso mean: 13.161 Å2 / Biso min: 5.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0 Å2-0 Å2
2---0.03 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms905 0 21 173 1099
Biso mean--17.02 26.67 -
Num. residues----117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.013949
X-RAY DIFFRACTIONr_bond_other_d0.0020.018830
X-RAY DIFFRACTIONr_angle_refined_deg1.7831.6761289
X-RAY DIFFRACTIONr_angle_other_deg1.5871.5991949
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4275117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.07824.850
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.68515156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.139154
X-RAY DIFFRACTIONr_chiral_restr0.0910.2125
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021072
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02181
X-RAY DIFFRACTIONr_rigid_bond_restr9.81431779
LS refinement shellResolution: 1→1.026 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 277 -
Rwork0.194 4918 -
all-5195 -
obs--99.92 %

+
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