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- PDB-6i1r: Crystal structure of CMP bound CST in an outward facing conformation -

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Basic information

Entry
Database: PDB / ID: 6i1r
TitleCrystal structure of CMP bound CST in an outward facing conformation
ComponentsCMP-sialic acid transporter 1
KeywordsMEMBRANE PROTEIN / CMP-sialic acid transporter / Secondary active transporter / Nucleotide sugar transporter / SLC35A1
Function / homology
Function and homology information


pyrimidine nucleotide-sugar transmembrane transporter activity / sialic acid transmembrane transporter activity / sialic acid transport / transmembrane transport / Golgi membrane / identical protein binding
Similarity search - Function
Nucleotide-sugar transporter / Nucleotide-sugar transporter
Similarity search - Domain/homology
CYTIDINE-5'-MONOPHOSPHATE / CMP-sialic acid transporter 1
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNji, E. / Gulati, A. / Qureshi, A.A. / Drew, D.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2019
Title: Structural basis for the delivery of activated sialic acid into Golgi for sialyation.
Authors: Nji, E. / Gulati, A. / Qureshi, A.A. / Coincon, M. / Drew, D.
History
DepositionOct 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CMP-sialic acid transporter 1
B: CMP-sialic acid transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6844
Polymers73,0382
Non-polymers6462
Water68538
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.379, 181.009, 53.081
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1 / Auth seq-ID: 1 - 313 / Label seq-ID: 1 - 313

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999959, -0.00049, 0.009094), (0.000581, -0.99995, 0.010026), (0.009089, 0.010031, 0.999908)-45.027889, -89.764793, 0.61438

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Components

#1: Protein CMP-sialic acid transporter 1


Mass: 36518.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: 100274139, ZEAMMB73_Zm00001d046060 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: B4FZ94
#2: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.16 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5
Details: 400 mM Ammonium sulfate, 100 mM Lithium sulfate, 100 mM NaCl, 100 mM Sodium citrate, 30% PEG 300, tert butanol and 1.2 mM CMP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 20716 / % possible obs: 100 % / Redundancy: 7 % / Rpim(I) all: 0.076 / Rrim(I) all: 0.201 / Rsym value: 0.185 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.8-2.957.21.9440.830210.7732.0941.944100
2.95-3.137.11.3651.228310.5461.4711.365100
3.13-3.357.10.8891.927080.3580.9590.889100
3.35-3.616.60.5073.224800.2130.5510.507100
3.61-3.967.20.256.623120.10.2690.25100
3.96-4.437.20.1311.720820.0520.140.13100
4.43-5.116.80.10814.318340.0450.1180.10899.9
5.11-6.266.90.11812.515600.0490.1280.118100
6.26-8.857.10.06219.312200.0250.0670.062100
8.85-45.7876.80.04326680.020.0450.0499.5

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Processing

Software
NameVersionClassification
REFMACrefinement
SCALA3.3.22data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5i20

5i20


Resolution: 2.8→45.83 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.925 / SU B: 10.686 / SU ML: 0.225 / SU R Cruickshank DPI: 5.5881 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 5.588 / ESU R Free: 0.36
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2528 1048 5.1 %RANDOM
Rwork0.2394 ---
obs0.2401 19661 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 140.76 Å2 / Biso mean: 71.742 Å2 / Biso min: 31.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.02 Å2
2---0.04 Å20 Å2
3---0.05 Å2
Refinement stepCycle: final / Resolution: 2.8→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4817 0 42 38 4897
Biso mean--131.29 51.31 -
Num. residues----619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0144981
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174589
X-RAY DIFFRACTIONr_angle_refined_deg0.8461.7176807
X-RAY DIFFRACTIONr_angle_other_deg0.3061.69210590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0535615
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.34421.282156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.45115755
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1891512
X-RAY DIFFRACTIONr_chiral_restr0.0340.2679
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025413
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021037
Refine LS restraints NCSNumber: 2384 / Type: TIGHT THERMAL / Rms dev position: 5.53 Å / Weight position: 0.5
LS refinement shellResolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.177 70 -
Rwork0.258 1445 -
all-1515 -
obs--99.74 %

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