[English] 日本語
Yorodumi
- PDB-4wmy: Structure of Human intelectin-1 in complex with allyl-beta-galact... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wmy
TitleStructure of Human intelectin-1 in complex with allyl-beta-galactofuranose
ComponentsIntelectin-1
KeywordsSUGAR BINDING PROTEIN / lectin / disulfide-linked / carbohydrate-binding / innate immunity / calcium / microbe-binding / microbe-specific / galactose / galactofuranose / diol
Function / homology
Function and homology information


response to nematode / oligosaccharide binding / Antimicrobial peptides / protein homotrimerization / side of membrane / positive regulation of D-glucose import / brush border membrane / receptor complex / positive regulation of protein phosphorylation / membrane raft ...response to nematode / oligosaccharide binding / Antimicrobial peptides / protein homotrimerization / side of membrane / positive regulation of D-glucose import / brush border membrane / receptor complex / positive regulation of protein phosphorylation / membrane raft / calcium ion binding / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile.
Similarity search - Domain/homology
prop-2-en-1-yl beta-D-galactofuranoside / Intelectin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.601 Å
AuthorsWangkanont, K. / Kiessling, L.L. / Forest, K.T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Recognition of microbial glycans by human intelectin-1.
Authors: Wesener, D.A. / Wangkanont, K. / McBride, R. / Song, X. / Kraft, M.B. / Hodges, H.L. / Zarling, L.C. / Splain, R.A. / Smith, D.F. / Cummings, R.D. / Paulson, J.C. / Forest, K.T. / Kiessling, L.L.
History
DepositionOct 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Aug 19, 2015Group: Data collection / Database references / Derived calculations
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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 / _chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 24, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 2.2Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,19810
Polymers68,5172
Non-polymers6818
Water11,097616
1
A: Intelectin-1
hetero molecules

A: Intelectin-1
hetero molecules

A: Intelectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,79715
Polymers102,7763
Non-polymers1,02112
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
2
B: Intelectin-1
hetero molecules

B: Intelectin-1
hetero molecules

B: Intelectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,79715
Polymers102,7763
Non-polymers1,02112
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Unit cell
Length a, b, c (Å)117.865, 117.865, 117.865
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-775-

HOH

21B-742-

HOH

31B-814-

HOH

41B-826-

HOH

DetailsThe biological assembly is a trimer. Application of the operations Z,X,Y and Y,Z,X will generate one trimer from the dimer in the asymmetric unit. The peripheral molecules correspond to another distinct trimer.

-
Components

#1: Protein Intelectin-1 / ITLN-1 / Endothelial lectin HL-1 / Galactofuranose-binding lectin / Intestinal lactoferrin receptor / Omentin


Mass: 34258.516 Da / Num. of mol.: 2 / Fragment: carbohydrate-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITLN1, INTL, ITLN, LFR, UNQ640/PRO1270 / Plasmid: pcDNA4 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q8WWA0
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-3S6 / prop-2-en-1-yl beta-D-galactofuranoside / prop-2-en-1-yl beta-D-galactoside / prop-2-en-1-yl D-galactoside / prop-2-en-1-yl galactoside


Type: D-saccharide / Mass: 220.220 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 616 / 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: 2.17 Å3/Da / Density % sol: 43.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 100 mM Bis-Tris, 25% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.00394 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 20, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00394 Å / Relative weight: 1
ReflectionResolution: 1.6→30.4 Å / Num. obs: 71869 / % possible obs: 100 % / Redundancy: 11.1 % / Biso Wilson estimate: 18.24 Å2 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.024 / Rrim(I) all: 0.082 / Χ2: 0.974 / Net I/av σ(I): 29.455 / Net I/σ(I): 9.7 / Num. measured all: 801024
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.6610.90.77371340.870.2450.8110.779100
1.66-1.72110.57570840.9250.1810.6030.807100
1.72-1.811.10.38771280.9650.1210.4060.823100
1.8-1.911.20.26871670.9820.0840.2810.849100
1.9-2.0211.20.18271320.9910.0570.1910.936100
2.02-2.1711.20.13471540.9940.0420.1411.109100
2.17-2.3911.30.09571710.9970.0290.0991.015100
2.39-2.7411.30.07472150.9980.0230.0781.008100
2.74-3.4511.30.06472410.9980.020.0681.339100
3.45-30.410.90.04574430.9990.0140.0471.05799.9

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 1.601→28.586 Å / FOM work R set: 0.8915 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1796 3578 4.98 %random
Rwork0.1546 68253 --
obs0.1559 71831 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.02 Å2 / Biso mean: 21.68 Å2 / Biso min: 7.89 Å2
Refinement stepCycle: final / Resolution: 1.601→28.586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4424 0 36 616 5076
Biso mean--30.7 32.55 -
Num. residues----564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014842
X-RAY DIFFRACTIONf_angle_d1.1196651
X-RAY DIFFRACTIONf_chiral_restr0.082638
X-RAY DIFFRACTIONf_plane_restr0.005875
X-RAY DIFFRACTIONf_dihedral_angle_d14.251746
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6007-1.65790.26383530.199967807133
1.6579-1.72430.21743620.18367877149
1.7243-1.80270.21223490.171767527101
1.8027-1.89770.19733540.16167907144
1.8977-2.01660.20283560.156867667122
2.0166-2.17230.18723590.147668137172
2.1723-2.39080.17873570.148367807137
2.3908-2.73650.18183560.153568567212
2.7365-3.44670.1743590.155868777236
3.4467-28.5910.15663730.146770527425

+
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