[English] 日本語
Yorodumi
- PDB-3rmw: Crystal Structure of Human Glycogenin-1 (GYG1) T83M mutant comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rmw
TitleCrystal Structure of Human Glycogenin-1 (GYG1) T83M mutant complexed with manganese and UDP-glucose
ComponentsGlycogenin-1
KeywordsTRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC / glycosyltransferase / glycogen biosynthesis / glycosylation
Function / homology
Function and homology information


Glycogen storage disease type XV (GYG1) / Glycogen storage disease type 0 (muscle GYS1) / glycogenin glucosyltransferase / Glycogen storage disease type II (GAA) / glycogenin glucosyltransferase activity / glycogen biosynthetic process / Glycogen breakdown (glycogenolysis) / glycosyltransferase activity / Myoclonic epilepsy of Lafora / Glycogen synthesis ...Glycogen storage disease type XV (GYG1) / Glycogen storage disease type 0 (muscle GYS1) / glycogenin glucosyltransferase / Glycogen storage disease type II (GAA) / glycogenin glucosyltransferase activity / glycogen biosynthetic process / Glycogen breakdown (glycogenolysis) / glycosyltransferase activity / Myoclonic epilepsy of Lafora / Glycogen synthesis / lysosomal lumen / manganese ion binding / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / protein homodimerization activity / extracellular region / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
: / Glycosyl transferase, family 8 / Glycosyl transferase family 8 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / URIDINE-5'-DIPHOSPHATE-GLUCOSE / Glycogenin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsChaikuad, A. / Froese, D.S. / Yue, W.W. / Krysztofinska, E. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Conformational plasticity of glycogenin and its maltosaccharide substrate during glycogen biogenesis.
Authors: Chaikuad, A. / Froese, D.S. / Berridge, G. / von Delft, F. / Oppermann, U. / Yue, W.W.
History
DepositionApr 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 28, 2011Group: Database references
Revision 1.3Jan 11, 2012Group: Database references
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_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_alt_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_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: Glycogenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,03216
Polymers29,6421
Non-polymers1,39015
Water3,405189
1
A: Glycogenin-1
hetero molecules

A: Glycogenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,06432
Polymers59,2832
Non-polymers2,78130
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area7920 Å2
ΔGint1 kcal/mol
Surface area22510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.650, 100.610, 49.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Glycogenin-1 / GN-1 / GN1


Mass: 29641.729 Da / Num. of mol.: 1 / Fragment: UNP residues 1-262 / Mutation: T83M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GYG, GYG1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 / References: UniProt: P46976, glycogenin glucosyltransferase

-
Non-polymers , 5 types, 204 molecules

#2: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.36 Å3/Da / Density % sol: 47.89 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 25% PEG smears (PEG 6k, 8k, 10k), 0.2M MgCl2, 10% glycerol, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 26, 2010
RadiationMonochromator: Flat graphite crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→29.85 Å / Num. all: 21806 / Num. obs: 21806 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 10.7
Reflection shellResolution: 1.93→2.03 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.728 / Mean I/σ(I) obs: 2 / Num. unique all: 3129 / % possible all: 100

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3Q4S

3q4s


Resolution: 1.93→28.86 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / SU B: 7.122 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.162 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23735 1116 5.1 %RANDOM
Rwork0.1841 ---
obs0.18674 20690 99.98 %-
all-21806 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.627 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å20 Å2
2---0.54 Å20 Å2
3---1.15 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.93→28.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1954 0 86 189 2229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222158
X-RAY DIFFRACTIONr_bond_other_d0.0030.021426
X-RAY DIFFRACTIONr_angle_refined_deg1.4042.0122924
X-RAY DIFFRACTIONr_angle_other_deg0.8233.0033443
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9475258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60224.35385
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.22415335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.575158
X-RAY DIFFRACTIONr_chiral_restr0.0920.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212267
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02412
X-RAY DIFFRACTIONr_mcbond_it0.841.51266
X-RAY DIFFRACTIONr_mcbond_other0.2221.5505
X-RAY DIFFRACTIONr_mcangle_it1.46422058
X-RAY DIFFRACTIONr_scbond_it2.2923892
X-RAY DIFFRACTIONr_scangle_it3.4784.5860
X-RAY DIFFRACTIONr_sphericity_free5.47631
X-RAY DIFFRACTIONr_sphericity_bonded5.3331
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 84 -
Rwork0.325 1487 -
obs--100 %
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)
12.03010.02530.66422.1253-0.42631.5327-0.0148-0.0654-0.093-0.02690.0435-0.00890.0729-0.0245-0.02870.01330.01380.00140.0181-0.00690.007617.291715.408611.562
219.3522-4.7534-0.060411.72917.715413.99010.29640.2099-1.07750.1132-0.15591.15260.6073-0.5363-0.14050.1215-0.0772-0.03790.11880.00170.19223.47978.50180.0435
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 233
2X-RAY DIFFRACTION2A242 - 262

+
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