[English] 日本語
Yorodumi
- PDB-6r2u: Zinc-alpha2-Glycoprotein with a Fluorescent Dansyl C 11 Fatty Acid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6r2u
TitleZinc-alpha2-Glycoprotein with a Fluorescent Dansyl C 11 Fatty Acid
ComponentsZinc-alpha-2-glycoprotein
KeywordsTRANSPORT PROTEIN / MHC Class I protein family. Fatty acid binding / Associated with obesity. Associated with type 2 diabetes.
Function / homology
Function and homology information


Miscellaneous transport and binding events / detection of chemical stimulus involved in sensory perception of bitter taste / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / protein transmembrane transporter activity / RNA nuclease activity / positive regulation of T cell mediated cytotoxicity / : / cell adhesion / immune response ...Miscellaneous transport and binding events / detection of chemical stimulus involved in sensory perception of bitter taste / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / protein transmembrane transporter activity / RNA nuclease activity / positive regulation of T cell mediated cytotoxicity / : / cell adhesion / immune response / negative regulation of cell population proliferation / external side of plasma membrane / extracellular space / extracellular exosome / extracellular region / nucleus
Similarity search - Function
MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-11D / AZIDE ION / Zinc-alpha-2-glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsLau, A.M. / Gor, J. / Perkins, S.J. / Coker, A.R. / McDermott, L.C.
CitationJournal: Biochem.J. / Year: 2019
Title: Crystal structure of zinc-alpha 2-glycoprotein in complex with a fatty acid reveals multiple different modes of protein-lipid binding.
Authors: Lau, A.M. / Zahid, H. / Gor, J. / Perkins, S.J. / Coker, A.R. / McDermott, L.C.
History
DepositionMar 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Zinc-alpha-2-glycoprotein
B: Zinc-alpha-2-glycoprotein
C: Zinc-alpha-2-glycoprotein
D: Zinc-alpha-2-glycoprotein
E: Zinc-alpha-2-glycoprotein
F: Zinc-alpha-2-glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,75429
Polymers193,8906
Non-polymers4,86423
Water1,982110
1
A: Zinc-alpha-2-glycoprotein
hetero molecules


  • defined by author
  • Evidence: equilibrium centrifugation, We are aware that a tetramer with a convincing beta-barrel exists in this crystal form. However, we have found no evidence of this in solution, including with ...Evidence: equilibrium centrifugation, We are aware that a tetramer with a convincing beta-barrel exists in this crystal form. However, we have found no evidence of this in solution, including with the same ligand and similar conditions to the crystallisation condition (without the precipitant). There is no reference to ZAG forming a tetramer in the literature and other ZAG structures in the PDB do not show it.
  • 33.1 kDa, 1 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)33,1346
Polymers32,3151
Non-polymers8195
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Zinc-alpha-2-glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8537
Polymers32,3151
Non-polymers1,5386
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Zinc-alpha-2-glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0385
Polymers32,3151
Non-polymers7234
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Zinc-alpha-2-glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0385
Polymers32,3151
Non-polymers7234
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Zinc-alpha-2-glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8463
Polymers32,3151
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Zinc-alpha-2-glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8463
Polymers32,3151
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.015, 167.015, 204.948
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPTRPTRPAA5 - 2756 - 276
21ASPASPTRPTRPBB5 - 2756 - 276
12ASPASPGLUGLUAA5 - 2766 - 277
22ASPASPGLUGLUCC5 - 2766 - 277
13ASPASPGLUGLUAA5 - 2766 - 277
23ASPASPGLUGLUDD5 - 2766 - 277
14ARGARGTRPTRPAA7 - 2758 - 276
24ARGARGTRPTRPEE7 - 2758 - 276
15ASPASPGLUGLUAA5 - 2766 - 277
25ASPASPGLUGLUFF5 - 2766 - 277
16ASPASPTRPTRPBB5 - 2756 - 276
26ASPASPTRPTRPCC5 - 2756 - 276
17ASPASPTRPTRPBB5 - 2756 - 276
27ASPASPTRPTRPDD5 - 2756 - 276
18ARGARGGLUGLUBB7 - 2768 - 277
28ARGARGGLUGLUEE7 - 2768 - 277
19ASPASPTRPTRPBB5 - 2756 - 276
29ASPASPTRPTRPFF5 - 2756 - 276
110ASPASPGLUGLUCC5 - 2766 - 277
210ASPASPGLUGLUDD5 - 2766 - 277
111ARGARGTRPTRPCC7 - 2758 - 276
211ARGARGTRPTRPEE7 - 2758 - 276
112ASPASPGLUGLUCC5 - 2766 - 277
212ASPASPGLUGLUFF5 - 2766 - 277
113ARGARGTRPTRPDD7 - 2758 - 276
213ARGARGTRPTRPEE7 - 2758 - 276
114ASPASPGLUGLUDD5 - 2766 - 277
214ASPASPGLUGLUFF5 - 2766 - 277
115ARGARGTRPTRPEE7 - 2758 - 276
215ARGARGTRPTRPFF7 - 2758 - 276

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

-
Components

#1: Protein
Zinc-alpha-2-glycoprotein / Zn-alpha-2-glycoprotein


Mass: 32315.072 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AZGP1, ZAG, ZNGP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25311
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-11D / 11-({[5-(dimethylamino)naphthalen-1-yl]sulfonyl}amino)undecanoic acid / 11-(Dansylamino)undecanoic acid


Mass: 434.592 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C23H34N2O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 3.7 Å3/Da / Density % sol: 66.73 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 1.3 M (NH4)2SO4, 100 mM Hepes

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.637
11-H, K, -L20.363
ReflectionResolution: 2.49→77.4 Å / Num. obs: 98002 / % possible obs: 100 % / Redundancy: 15.3 % / Biso Wilson estimate: 51.29 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.054 / Rrim(I) all: 0.212 / Net I/σ(I): 10
Reflection shellResolution: 2.49→2.53 Å / Redundancy: 15.6 % / Mean I/σ(I) obs: 1 / Num. unique obs: 4802 / CC1/2: 0.298 / Rpim(I) all: 0.856 / Rrim(I) all: 3.388 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1t7v, pdbredo

1t7v


Resolution: 2.49→77.4 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.83 / SU ML: 0.095 / Cross valid method: FREE R-VALUE / ESU R: 0.054 / ESU R Free: 0.043 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21202 2698 2.8 %RANDOM
Rwork0.17019 ---
obs0.17126 95132 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 62.751 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å2-0 Å2-0 Å2
2---0.3 Å2-0 Å2
3---0.59 Å2
Refinement stepCycle: 1 / Resolution: 2.49→77.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13369 0 313 110 13792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01914083
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212387
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.93719127
X-RAY DIFFRACTIONr_angle_other_deg0.954328899
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08551627
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54624.492719
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.505152268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3751572
X-RAY DIFFRACTIONr_chiral_restr0.1020.21909
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02116077
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022943
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.566.1636526
X-RAY DIFFRACTIONr_mcbond_other4.566.1626525
X-RAY DIFFRACTIONr_mcangle_it6.5979.2498147
X-RAY DIFFRACTIONr_mcangle_other6.5979.258148
X-RAY DIFFRACTIONr_scbond_it4.6316.6087557
X-RAY DIFFRACTIONr_scbond_other4.636.6087556
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7259.75510981
X-RAY DIFFRACTIONr_long_range_B_refined9.22469.80814995
X-RAY DIFFRACTIONr_long_range_B_other9.22469.8114996
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A173820.08
12B173820.08
21A174940.08
22C174940.08
31A176520.07
32D176520.07
41A174080.08
42E174080.08
51A176060.07
52F176060.07
61B173240.09
62C173240.09
71B174660.08
72D174660.08
81B173760.08
82E173760.08
91B173880.08
92F173880.08
101C176160.08
102D176160.08
111C173560.08
112E173560.08
121C175040.08
122F175040.08
131D174760.08
132E174760.08
141D176640.08
142F176640.08
151E174980.08
152F174980.08
LS refinement shellResolution: 2.49→2.555 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 161 -
Rwork0.251 7013 -
obs--99.85 %

+
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