[English] 日本語
- PDB-6oh4: X-ray crystal structure of the mouse CMP-sialic acid transporter ... -

Open data

ID or keywords:


Basic information

Database: PDB / ID: 6oh4
TitleX-ray crystal structure of the mouse CMP-sialic acid transporter in complex with CMP, by hanging drop vapor diffusion
ComponentsCMP-sialic acid transporter
KeywordsTRANSPORT PROTEIN / drug/metabolite transporter / nucleotide-sugar / sialic acid / glycosylation
Function / homology
Function and homology information

CMP-N-acetylneuraminate transmembrane transporter activity / UDP-galactose transmembrane transporter activity / CMP-N-acetylneuraminate transmembrane transport / Transport of nucleotide sugars / Sialic acid metabolism / antiporter activity / integral component of Golgi membrane / carbohydrate transport / integral component of membrane
Similarity search - Function
Nucleotide-sugar transporter / Nucleotide-sugar transporter
Similarity search - Domain/homology
CYTIDINE-5'-MONOPHOSPHATE / CMP-sialic acid transporter
Similarity search - Component
Biological speciesMus musculus (house mouse)
AuthorsAhuja, S. / Whorton, M.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM130909 United States
CitationJournal: Elife / Year: 2019
Title: Structural basis for mammalian nucleotide sugar transport.
Authors: Ahuja, S. / Whorton, M.R.
DepositionApr 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

Structure visualization

Structure viewerMolecule:

Downloads & links


Deposited unit
A: CMP-sialic acid transporter
B: CMP-sialic acid transporter
hetero molecules

Theoretical massNumber of molelcules
Total (without water)75,6364
A: CMP-sialic acid transporter
hetero molecules

Theoretical massNumber of molelcules
Total (without water)37,8182
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
B: CMP-sialic acid transporter
hetero molecules

Theoretical massNumber of molelcules
Total (without water)37,8182
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.820, 193.960, 66.440
Angle α, β, γ (deg.)90.00, 101.79, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A15 - 317
2010B15 - 317
DetailsThe authors state that there are no biologically relevant macromolecular assemblies in this structure.


#1: Protein CMP-sialic acid transporter / / CMP-Sia-Tr / Solute carrier family 35 member A1

Mass: 37494.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Slc35a1 / Production host: Komagataella pastoris (fungus) / Strain (production host): SMD1168H / References: UniProt: Q61420
#2: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE / Cytidine monophosphate

Mass: 323.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O8P / Feature type: SUBJECT OF INVESTIGATION

Experimental details


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

Sample preparation

CrystalDensity Matthews: 4.36 Å3/Da / Density % sol: 71.78 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25.6-26.8% PEG 400, 0.1 M Tris pH 8.5, and 0.1 M magnesium acetate

Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03313 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03313 Å / Relative weight: 1
ReflectionResolution: 3.38→49 Å / Num. obs: 11456 / % possible obs: 67.3 % / Redundancy: 3.6 % / Net I/σ(I): 6.7
Reflection shellResolution: 3.38→3.5 Å / Num. unique obs: 51


XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 3.38→49 Å / Cor.coef. Fo:Fc: 0.761 / Cor.coef. Fo:Fc free: 0.691 / SU B: 53.451 / SU ML: 0.765 / Cross valid method: THROUGHOUT / ESU R Free: 0.79 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32106 573 4.8 %RANDOM
Rwork0.28942 ---
obs0.29094 11456 67.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 143.981 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å2-0 Å20.84 Å2
2---1.5 Å2-0 Å2
3---1.43 Å2
Refinement stepCycle: 1 / Resolution: 3.38→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4460 0 42 0 4502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.024590
X-RAY DIFFRACTIONr_bond_other_d0.0010.024465
X-RAY DIFFRACTIONr_angle_refined_deg1.0111.9866271
X-RAY DIFFRACTIONr_angle_other_deg0.83310243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.65594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.62722.913127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64515722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.3881510
X-RAY DIFFRACTIONr_chiral_restr0.0450.2798
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024978
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02958
X-RAY DIFFRACTIONr_nbd_refined
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_it3.55914.8572388
X-RAY DIFFRACTIONr_mcbond_other3.55914.8562387
X-RAY DIFFRACTIONr_mcangle_it6.06422.272978
X-RAY DIFFRACTIONr_mcangle_other6.06322.2712979
X-RAY DIFFRACTIONr_scbond_it3.10514.9692202
X-RAY DIFFRACTIONr_scbond_other3.10314.9722198
X-RAY DIFFRACTIONr_scangle_other5.60722.4213288
X-RAY DIFFRACTIONr_long_range_B_refined9.4925230
X-RAY DIFFRACTIONr_long_range_B_other9.4935231
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 19128 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0 Å / Weight position: 0.05

Dom-IDAuth asym-ID
LS refinement shellResolution: 3.384→3.472 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.14 2 -
Rwork0.335 51 -
obs--3.93 %

About Yorodumi


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

Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search


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