[English] 日本語
Yorodumi
- PDB-4han: Crystal structure of Galectin 8 with NDP52 peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4han
TitleCrystal structure of Galectin 8 with NDP52 peptide
Components
  • Calcium-binding and coiled-coil domain-containing protein 2
  • Galectin-8
KeywordsSUGAR BINDING PROTEIN / Autophagy / innate immunity / carbohydrate recognition domain (CRD) / autophagy adapter molecule / NAD binding / NDP52 peoptide binding / Cytosol
Function / homology
Function and homology information


lymphatic endothelial cell migration / xenophagy / positive regulation of autophagosome maturation / response to type II interferon / autophagosome membrane / viral process / autophagosome / PML body / cellular response to virus / integrin binding ...lymphatic endothelial cell migration / xenophagy / positive regulation of autophagosome maturation / response to type II interferon / autophagosome membrane / viral process / autophagosome / PML body / cellular response to virus / integrin binding / carbohydrate binding / cytoplasmic vesicle / cytoskeleton / intracellular membrane-bounded organelle / perinuclear region of cytoplasm / protein homodimerization activity / extracellular space / membrane / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
SKICH domain / : / SKICH domain / CALCOCO1/2, zinc finger UBZ1-type / Zinc finger UBZ1-type profile. / Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin ...SKICH domain / : / SKICH domain / CALCOCO1/2, zinc finger UBZ1-type / Zinc finger UBZ1-type profile. / Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Galectin-8 / Calcium-binding and coiled-coil domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.551 Å
AuthorsKim, B.-W. / Hong, S.B. / Kim, J.H. / Kwon, D.H. / Song, H.K.
CitationJournal: Nat Commun / Year: 2013
Title: Structural basis for recognition of autophagic receptor NDP52 by the sugar receptor galectin-8.
Authors: Kim, B.W. / Hong, S.B. / Kim, J.H. / Kwon, D.H. / Song, H.K.
History
DepositionSep 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Jul 26, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Galectin-8
B: Galectin-8
C: Calcium-binding and coiled-coil domain-containing protein 2
D: Calcium-binding and coiled-coil domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0219
Polymers69,3764
Non-polymers1,6455
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-8 kcal/mol
Surface area27240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.884, 71.884, 314.493
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

-
Components

#1: Protein Galectin-8


Mass: 33222.207 Da / Num. of mol.: 2 / Fragment: UNP residues 1-155. 184-317
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: O00214
#2: Protein/peptide Calcium-binding and coiled-coil domain-containing protein 2 / Antigen nuclear dot 52 kDa protein / Nuclear domain 10 protein NDP52 / Nuclear domain 10 protein 52 ...Antigen nuclear dot 52 kDa protein / Nuclear domain 10 protein NDP52 / Nuclear domain 10 protein 52 / Nuclear dot protein 52


Mass: 1465.564 Da / Num. of mol.: 2 / Fragment: UNP residues 372-385
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALCOCO2, NDP52 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13137
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 3.38 Å3/Da / Density % sol: 63.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-Hcl pH8.5, 30~34% (v/w) PEG400, 200mM LiSO4, and 10mM Nicotinamide adenine dinucleotide, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 16, 2012
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.55→40.1 Å / Num. obs: 30888 / % possible obs: 99.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.551→40.096 Å / SU ML: 0.23 / σ(F): 0 / Phase error: 22.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2138 1977 6.49 %Random
Rwork0.1913 ---
obs0.1928 30450 98.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.551→40.096 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4781 0 109 351 5241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085031
X-RAY DIFFRACTIONf_angle_d1.5326824
X-RAY DIFFRACTIONf_dihedral_angle_d15.4751845
X-RAY DIFFRACTIONf_chiral_restr0.139746
X-RAY DIFFRACTIONf_plane_restr0.004874
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5507-2.61450.30091320.25141955X-RAY DIFFRACTION95
2.6145-2.68510.25831320.24261966X-RAY DIFFRACTION96
2.6851-2.76410.30371400.23292004X-RAY DIFFRACTION96
2.7641-2.85330.26011330.22681943X-RAY DIFFRACTION97
2.8533-2.95530.2551390.2231992X-RAY DIFFRACTION98
2.9553-3.07360.21551390.22272015X-RAY DIFFRACTION98
3.0736-3.21340.24281350.21332035X-RAY DIFFRACTION99
3.2134-3.38270.26041410.20242050X-RAY DIFFRACTION100
3.3827-3.59450.19671450.18212082X-RAY DIFFRACTION100
3.5945-3.87190.23641430.17762037X-RAY DIFFRACTION100
3.8719-4.26110.18511450.162074X-RAY DIFFRACTION100
4.2611-4.87680.16191490.14442059X-RAY DIFFRACTION100
4.8768-6.14070.19661510.18712108X-RAY DIFFRACTION100
6.1407-40.10080.19431530.20582153X-RAY DIFFRACTION99
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)
16.3648-0.0978-1.64920.6302-1.50763.7103-0.0761-0.3093-0.08660.04570.1414-0.03560.22170.0757-0.0280.3220.0507-0.02240.3222-0.12020.414723.1528-6.0774336.6088
21.39530.24510.73472.7024-0.69952.61760.0677-0.20550.1759-0.08360.00670.1311-0.3301-0.0618-0.06160.34940.11460.04680.3786-0.13480.431626.18221.9484323.4845
34.206-0.3559-0.46913.12150.25432.80890.08040.3922-0.3308-0.0801-0.14740.21110.1492-0.74350.06510.2771-0.01670.05360.6094-0.0630.3587-5.6022-9.8489347.2401
41.64050.58670.71541.24950.21272.51970.119-0.029-0.0304-0.1515-0.0211-0.1139-0.1170.1652-0.07770.25270.07860.1210.42670.02150.417723.63491.8234355.9302
53.5675-1.0117-0.60883.23130.60613.0882-0.218-0.2244-0.37320.21370.11970.15650.73840.22810.05580.55480.12180.07810.3346-0.00160.374330.2312-30.5188334.067
61.3878-2.4205-1.80564.90014.16783.8071-0.15040.16180.3412-0.10.3177-0.0317-0.3908-0.318-0.16680.65010.29970.07830.8410.07330.3309-2.6750.114334.6043
70.11460.1811-0.17840.86450.43013.76660.04710.41310.01340.11590.1812-0.1514-0.22460.1090.11650.47920.1249-0.19711.1741-0.12580.176237.268-22.9752346.7688
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 155 )
3X-RAY DIFFRACTION3chain 'A' and (resid 156 through 291 )
4X-RAY DIFFRACTION4chain 'B' and (resid -1 through 155 )
5X-RAY DIFFRACTION5chain 'B' and (resid 156 through 291 )
6X-RAY DIFFRACTION6chain 'C' and (resid 372 through 380 )
7X-RAY DIFFRACTION7chain 'D' and (resid 372 through 380 )

+
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