[English] 日本語
Yorodumi
- PDB-6zdc: Structure of the catalytic domain of human endo-alpha-mannosidase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zdc
TitleStructure of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with nickel
ComponentsGlycoprotein endo-alpha-1,2-mannosidase
KeywordsHYDROLASE / Golgi / mannosidase / retaining
Function / homology
Function and homology information


glycoprotein endo-alpha-1,2-mannosidase / glycoprotein endo-alpha-1,2-mannosidase activity / N-glycan trimming and elongation in the cis-Golgi / alpha-mannosidase activity / Golgi membrane / Golgi apparatus
Similarity search - Function
Glycosyl hydrolase family 99 / Glycosyl hydrolase family 99 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
NICKEL (II) ION / Glycoprotein endo-alpha-1,2-mannosidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.251 Å
AuthorsSobala, L.F. / Fernandes, P.Z. / Hakki, Z. / Thompson, A.J. / Howe, J.D. / Hill, M. / Zitzmann, N. / Davies, S. / Stamataki, Z. / Butters, T.D. ...Sobala, L.F. / Fernandes, P.Z. / Hakki, Z. / Thompson, A.J. / Howe, J.D. / Hill, M. / Zitzmann, N. / Davies, S. / Stamataki, Z. / Butters, T.D. / Alonzi, D.S. / Williams, S.J. / Davies, G.J.
Funding support United Kingdom, Australia, 4items
OrganizationGrant numberCountry
European Research Council (ERC)322942 United Kingdom
Australian Research Council (ARC)DP120101396 Australia
Australian Research Council (ARC)FT130100103 Australia
Australian Research Council (ARC)DP180101957 Australia
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structure of human endo-alpha-1,2-mannosidase (MANEA), an antiviral host-glycosylation target.
Authors: Sobala, L.F. / Fernandes, P.Z. / Hakki, Z. / Thompson, A.J. / Howe, J.D. / Hill, M. / Zitzmann, N. / Davies, S. / Stamataki, Z. / Butters, T.D. / Alonzi, D.S. / Williams, S.J. / Davies, G.J.
History
DepositionJun 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 20, 2021Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Jan 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycoprotein endo-alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8422
Polymers44,7831
Non-polymers591
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-5 kcal/mol
Surface area15420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.467, 86.535, 135.916
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

-
Components

#1: Protein Glycoprotein endo-alpha-1,2-mannosidase / / hEndo / Mandaselin


Mass: 44783.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MANEA / Plasmid: pCold-I / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q5SRI9, glycoprotein endo-alpha-1,2-mannosidase
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100 mM MIB buffer, pH 6.0. Protein at 5.5 mg/ml in 50 mM potassium phosphate, 50 mM KCl. 150 nl protein solution and 150 nl reservoir solution.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.25→135.92 Å / Num. obs: 21876 / % possible obs: 98.1 % / Redundancy: 11.4 % / Biso Wilson estimate: 40.95 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.061 / Rrim(I) all: 0.21 / Net I/σ(I): 7
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.872 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1648 / CC1/2: 0.345 / Rpim(I) all: 0.75 / Rrim(I) all: 2.029 / % possible all: 84.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALS1.4.1-gba385ba-releasedata reduction
Aimless0.5.31data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M17

5m17


Resolution: 2.251→73.103 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.223 / WRfactor Rwork: 0.171 / Average fsc free: 0.8875 / Average fsc work: 0.9025 / Cross valid method: THROUGHOUT / ESU R: 0.249 / ESU R Free: 0.199
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2234 1106 5.069 %RANDOM
Rwork0.1769 20711 --
all0.179 ---
obs-21817 97.764 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 47.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.734 Å2-0 Å2-0 Å2
2---2.644 Å20 Å2
3---3.378 Å2
Refinement stepCycle: LAST / Resolution: 2.251→73.103 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2877 0 1 183 3061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0133007
X-RAY DIFFRACTIONr_bond_other_d0.0350.0172628
X-RAY DIFFRACTIONr_angle_refined_deg1.8891.6554097
X-RAY DIFFRACTIONr_angle_other_deg2.3411.5756121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4945358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.04121.916167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.07215480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7861517
X-RAY DIFFRACTIONr_chiral_restr0.1340.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023371
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02684
X-RAY DIFFRACTIONr_nbd_refined0.2020.2634
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.22557
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21492
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21399
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2173
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1120.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2080.220
X-RAY DIFFRACTIONr_nbd_other0.2460.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1760.211
X-RAY DIFFRACTIONr_mcbond_it3.4125.0021408
X-RAY DIFFRACTIONr_mcbond_other3.4084.9981407
X-RAY DIFFRACTIONr_mcangle_it5.3387.4781759
X-RAY DIFFRACTIONr_mcangle_other5.3377.4821760
X-RAY DIFFRACTIONr_scbond_it3.475.1951598
X-RAY DIFFRACTIONr_scbond_other3.4695.1981599
X-RAY DIFFRACTIONr_scangle_it5.5297.6782333
X-RAY DIFFRACTIONr_scangle_other5.5277.6812334
X-RAY DIFFRACTIONr_lrange_it8.16156.5393584
X-RAY DIFFRACTIONr_lrange_other8.11656.4553561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.251-2.310.344660.3361231X-RAY DIFFRACTION81.0625
2.31-2.3730.326830.3091353X-RAY DIFFRACTION91.1746
2.373-2.4420.312720.2881444X-RAY DIFFRACTION97.8696
2.442-2.5170.279680.2441396X-RAY DIFFRACTION99.3216
2.517-2.5990.244850.2161371X-RAY DIFFRACTION100
2.599-2.690.271600.2111343X-RAY DIFFRACTION100
2.69-2.7920.283770.2041290X-RAY DIFFRACTION99.9269
2.792-2.9060.279790.1871222X-RAY DIFFRACTION99.9232
2.906-3.0350.24590.1831181X-RAY DIFFRACTION100
3.035-3.1830.225780.1721155X-RAY DIFFRACTION100
3.183-3.3550.226430.161101X-RAY DIFFRACTION100
3.355-3.5590.236560.1891024X-RAY DIFFRACTION100
3.559-3.8040.228540.173993X-RAY DIFFRACTION100
3.804-4.1090.236410.165924X-RAY DIFFRACTION99.7932
4.109-4.50.19400.13848X-RAY DIFFRACTION100
4.5-5.0310.161320.113786X-RAY DIFFRACTION99.7561
5.031-5.8080.194450.128679X-RAY DIFFRACTION100
5.808-7.110.167270.146601X-RAY DIFFRACTION100
7.11-10.0410.153230.133480X-RAY DIFFRACTION100
10.041-73.1030.142180.213289X-RAY DIFFRACTION99.3528

+
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