[English] 日本語
Yorodumi
- PDB-3hr0: Crystal structure of Homo sapiens Conserved Oligomeric Golgi subunit 4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hr0
TitleCrystal structure of Homo sapiens Conserved Oligomeric Golgi subunit 4
ComponentsCoG4
KeywordsTRANSPORT PROTEIN / Conserved oligomeric Golgi complex / intracellular trafficking / vesicle tethering / multisubunit tethering complex / exocyst / Alternative splicing / Golgi apparatus / Membrane / Phosphoprotein / Protein transport / Transport
Function / homology
Function and homology information


retrograde transport, vesicle recycling within Golgi / glycosylation / Golgi transport complex / Retrograde transport at the Trans-Golgi-Network / Intra-Golgi traffic / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / Golgi organization / COPI-mediated anterograde transport / trans-Golgi network membrane / protein transport ...retrograde transport, vesicle recycling within Golgi / glycosylation / Golgi transport complex / Retrograde transport at the Trans-Golgi-Network / Intra-Golgi traffic / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / Golgi organization / COPI-mediated anterograde transport / trans-Golgi network membrane / protein transport / Golgi membrane / identical protein binding / cytosol
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1970 / Conserved oligomeric Golgi complex, subunit 4 / : / : / : / COG4 transport protein, middle alpha-helical bundle / Conserved oligomeric Golgi complex subunit 4, C-terminal / Conserved oligomeric Golgi complex subunit 4, N-terminal / COG4 transport protein / ESAT-6-like ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1970 / Conserved oligomeric Golgi complex, subunit 4 / : / : / : / COG4 transport protein, middle alpha-helical bundle / Conserved oligomeric Golgi complex subunit 4, C-terminal / Conserved oligomeric Golgi complex subunit 4, N-terminal / COG4 transport protein / ESAT-6-like / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Conserved oligomeric Golgi complex subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsRichardson, B.C. / Ungar, D. / Nakamura, A. / Jeffrey, P.D. / Hughson, F.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structural basis for a human glycosylation disorder caused by mutation of the COG4 gene.
Authors: Richardson, B.C. / Smith, R.D. / Ungar, D. / Nakamura, A. / Jeffrey, P.D. / Lupashin, V.V. / Hughson, F.M.
History
DepositionJun 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
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_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CoG4
B: CoG4


Theoretical massNumber of molelcules
Total (without water)59,5772
Polymers59,5772
Non-polymers00
Water6,936385
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-35 kcal/mol
Surface area24420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.114, 87.114, 214.773
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRTHRTHRAA537 - 71915 - 197
21THRTHRTHRTHRBB537 - 71915 - 197
12TRPTRPLEULEUAA758 - 785236 - 263
22TRPTRPLEULEUBB758 - 785236 - 263
13ILEILETRPTRPAA723 - 749201 - 227
23ILEILETRPTRPBB723 - 749201 - 227

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein CoG4 / Conserved oligomeric Golgi complex subunit 4 / Component of oligomeric Golgi complex 4


Mass: 29788.740 Da / Num. of mol.: 2 / Fragment: Residues 525-785
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COG4, COG4 / Plasmid: pDU01 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H9E3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 3.95 Å3/Da / Density % sol: 68.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 5% PEG-4000, 10 mM ammonium nitrate, 2.5% glycerol, 12 mM DTT, 10 mM Tris, 150 mM potassium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A11.0809
SYNCHROTRONNSLS X29A20.9792,0.9794,0.9611
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDApr 24, 2007
ADSC QUANTUM 3152CCDApr 24, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.08091
20.97921
30.97941
40.96111
ReflectionRedundancy: 5.2 % / Av σ(I) over netI: 26.48 / Number: 479448 / Rmerge(I) obs: 0.068 / Χ2: 1.01 / D res high: 2.2 Å / D res low: 100 Å / Num. obs: 92524 / % possible obs: 99.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.7410099.710.0320.7675.6
3.764.7410010.0491.2545.6
3.293.7610010.0581.0685.7
2.993.2910010.0790.9725.7
2.772.9910010.1351.0135.7
2.612.7710010.2161.0265.7
2.482.6110010.3111.0435.6
2.372.4810010.4281.0145.1
2.282.3799.410.5320.9894.1
2.22.2893.510.6560.9352.9
ReflectionResolution: 1.9→100 Å / Num. obs: 74854 / % possible obs: 99.3 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.077 / Χ2: 1.374 / Net I/σ(I): 26.485
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.975.10.35772790.76598.2
1.97-2.0550.23873370.84198.5
2.05-2.1450.17473410.9498.8
2.14-2.2550.13574141.03899.4
2.25-2.3950.10874511.11999.7
2.39-2.585.10.08974921.18899.9
2.58-2.845.40.07975051.35599.8
2.84-3.255.70.07975611.96899.9
3.25-4.096.20.07576302.22199.9
4.09-1006.60.06178441.73498.5

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT3.006data extraction
CBASSdata collection
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→30.59 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.343 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.222 3753 5 %RANDOM
Rwork0.194 ---
obs0.196 74786 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.01 Å2 / Biso mean: 29.464 Å2 / Biso min: 13.44 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3990 0 0 385 4375
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224019
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1911.9655453
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr
X-RAY DIFFRACTIONr_gen_planes_refined
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1732MEDIUM POSITIONAL0.630.5
1690LOOSE POSITIONAL0.795
1732MEDIUM THERMAL1.432
1690LOOSE THERMAL2.6710
2112MEDIUM POSITIONAL0.180.5
2124LOOSE POSITIONAL0.75
2112MEDIUM THERMAL12
2124LOOSE THERMAL3.4410
3108MEDIUM POSITIONAL0.130.5
3117LOOSE POSITIONAL0.615
3108MEDIUM THERMAL1.882
3117LOOSE THERMAL3.7110
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 269 -
Rwork0.237 5102 -
all-5371 -
obs--98.01 %

+
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