[English] 日本語
Yorodumi
- PDB-1ukm: Crystal structure of EMS16, an Antagonist of collagen receptor in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ukm
TitleCrystal structure of EMS16, an Antagonist of collagen receptor integrin alpha2beta1 (GPIa/IIa)
Components
  • EMS16 A chain
  • EMS16 B chain
KeywordsTOXIN / Domain swapping / C-type lectin
Function / homology
Function and homology information


toxin activity / extracellular region
Similarity search - Function
: / 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
Snaclec EMS16 subunit beta / Snaclec EMS16 subunit alpha
Similarity search - Component
Biological speciesEchis multisquamatus (snake)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHorii, K. / Okuda, D. / Morita, T. / Mizuno, H.
Citation
Journal: Biochemistry / Year: 2003
Title: Structural characterization of EMS16, an Antagonist of collagen receptor (GPIa/IIa) from the venom of Echis multisquamatus
Authors: Horii, K. / Okuda, D. / Morita, T. / Mizuno, H.
#1: Journal: J.BIOCHEM.(TOKYO) / Year: 2003
Title: Characterization and Preliminary Crystallographic Studies of EMS16, an Antagonist of Collagen Receptor (GPIa/IIa) from the Venom of Echis multisquamatus
Authors: Okuda, D. / Horii, K. / Mizuno, H. / Morita, T.
#2: Journal: Biochemistry / Year: 2000
Title: Isolation and characterization of EMS16, a C-lectin type protein from Echis multisquamatus venom, a potent and selective inhibitor of the alpha2beta1 integrin
Authors: Marcinkiewicz, C. / Lobb, R.R. / Marcinkiewicz, M.M. / Daniel, J.L. / Smith, J.B. / Dangelmaier, C. / Weinreb, P.H. / Beacham, D.A. / Niewiarowski, S.
History
DepositionAug 27, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jul 25, 2018Group: Data collection / Database references / Structure summary
Category: pdbx_entry_details / struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5Jul 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_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Oct 25, 2023Group: 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 1.7Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.8Oct 29, 2025Group: Database references / Structure summary / Category: entity / struct_ref_seq_dif / Item: _entity.pdbx_mutation / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EMS16 A chain
B: EMS16 B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6368
Polymers31,0112
Non-polymers6256
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-21 kcal/mol
Surface area12930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.570, 59.933, 115.743
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein EMS16 A chain / EMS16 subunit A


Mass: 15889.537 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-134 / Source method: isolated from a natural source / Source: (natural) Echis multisquamatus (snake) / Secretion: venom / References: UniProt: Q7T2Q1
#2: Protein EMS16 B chain / EMS16 subunit B


Mass: 15121.384 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-128 / Source method: isolated from a natural source / Source: (natural) Echis multisquamatus (snake) / Secretion: venom / References: UniProt: Q7T2Q0

-
Sugars , 1 types, 1 molecules

#5: 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

-
Non-polymers , 3 types, 255 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Sequence detailsThe sequence database UNP Q7T2Q0 reports there is a conflict as Experimental Information.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: PEG8000, potassium dihydrogen phosphate, glycerol, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 293 K / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
250 mMTris-HCl1droppH7.5
30.04 Mpotassium dihydrogen phosphate1reservoir
416 %PEG80001reservoir
520 %glycerol1reservoir

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 12, 2002 / Details: Osmic confocal mirrors
RadiationMonochromator: Osmic confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→29.71 Å / Num. obs: 26199 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 16.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 5.6 / % possible all: 99.7
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 91401
Reflection shell
*PLUS
% possible obs: 99.7 %

-
Processing

Software
NameVersionClassification
CNS1.1refinement
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BJ3

1bj3


Resolution: 1.9→18.36 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1271064.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1303 5 %RANDOM
Rwork0.196 ---
obs0.196 26143 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.6729 Å2 / ksol: 0.394865 e/Å3
Displacement parametersBiso mean: 27.7 Å2
Baniso -1Baniso -2Baniso -3
1-4.12 Å20 Å20 Å2
2---1.31 Å20 Å2
3----2.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.9→18.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2126 0 39 250 2415
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.21.5
X-RAY DIFFRACTIONc_mcangle_it3.842
X-RAY DIFFRACTIONc_scbond_it4.662
X-RAY DIFFRACTIONc_scangle_it6.272.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.334 209 4.9 %
Rwork0.274 4092 -
obs-4301 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2HETERO.PARAMHETERO.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5CARBO_REP.PARAMCARBOHYDRATE.TOP
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81

+
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