[English] 日本語
Yorodumi
- PDB-4jre: Crystal structure of nitrate/nitrite exchanger NarK with nitrite bound -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jre
TitleCrystal structure of nitrate/nitrite exchanger NarK with nitrite bound
Components
  • (Immunoglobulin ...Antibody) x 2
  • Nitrite extrusion protein 1
KeywordsTRANSPORT PROTEIN/Immune System / Transporter / Immunoglobulin / Major Facilitator Superfamily / Exchanger / TRANSPORT PROTEIN-Immune System complex
Function / homology
Function and homology information


nitrite transmembrane transporter activity / nitrate transmembrane transport / nitrite transport / nitrate transmembrane transporter activity / nitrate catabolic process / solute:inorganic anion antiporter activity / nitrate assimilation / plasma membrane
Similarity search - Function
Nitrate transporter NarK/NarU-like / Nitrate transporter / MFS general substrate transporter like domains / Major facilitator superfamily / Major Facilitator Superfamily / Growth Hormone; Chain: A; / MFS transporter superfamily / Immunoglobulins / Up-down Bundle / Immunoglobulin-like ...Nitrate transporter NarK/NarU-like / Nitrate transporter / MFS general substrate transporter like domains / Major facilitator superfamily / Major Facilitator Superfamily / Growth Hormone; Chain: A; / MFS transporter superfamily / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
methyl alpha-D-glucopyranoside / NITRITE ION / Nitrate/nitrite antiporter NarK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZheng, H. / Wisedchaisri, G. / Gonen, T.
CitationJournal: Nature / Year: 2013
Title: Crystal structure of a nitrate/nitrite exchanger.
Authors: Zheng, H. / Wisedchaisri, G. / Gonen, T.
History
DepositionMar 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Jul 10, 2013Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nitrite extrusion protein 1
B: Immunoglobulin Gamma-2a, Heavy chain
C: Immunoglobulin Kappa, Light chain
D: Nitrite extrusion protein 1
H: Immunoglobulin Gamma-2a, Heavy chain
L: Immunoglobulin Kappa, Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,40810
Polymers192,9286
Non-polymers4804
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.910, 81.407, 138.487
Angle α, β, γ (deg.)100.07, 96.38, 115.92
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.438432, 0.898763, 0.0016), (0.898761, 0.438435, -0.001679), (-0.002211, 0.000702, -0.999997)-29.88292, -32.48515, -128.24704

-
Components

-
Antibody , 2 types, 4 molecules BHCL

#2: Antibody Immunoglobulin Gamma-2a, Heavy chain


Mass: 23188.961 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: hybridoma
#3: Antibody Immunoglobulin Kappa, Light chain


Mass: 23265.705 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: hybridoma

-
Protein / Sugars , 2 types, 4 molecules AD

#1: Protein Nitrite extrusion protein 1 / Nitrite facilitator 1


Mass: 50009.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1223, JW1214, narK / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) C41 / References: UniProt: P10903
#5: Sugar ChemComp-GYP / methyl alpha-D-glucopyranoside / METHYL-ALPHA-D-GLUCOPYRANOSIDE / ALPHA-METHYL-D-GLUCOPYRANOSIDE / methyl alpha-D-glucoside / methyl D-glucoside / methyl glucoside / Methyl group


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C7H14O6
IdentifierTypeProgram
DGlcp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-glucopyranoseCOMMON NAMEGMML 1.0
methyl-a-D-glucopyranosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Non-polymers , 2 types, 37 molecules

#4: Chemical ChemComp-NO2 / NITRITE ION / Nitrite


Mass: 46.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 4.14 Å3/Da / Density % sol: 70.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 28% PEG400, 0.1 M citric acid pH 3.5, 0.1M NaCl and 0.1M Li2SO4. The crystal was subsequently soaked with 50mM NaNO2 in the above solution prior to freezing, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99999 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 9, 2012
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 72283 / % possible obs: 94.6 % / Observed criterion σ(I): 1.1 / Redundancy: 3.6 % / Biso Wilson estimate: 57.7 Å2 / Rsym value: 0.158 / Net I/σ(I): 7.9
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.1 / Num. unique all: 2893 / Rsym value: 0.866 / % possible all: 76.3

-
Processing

Software
NameVersionClassification
BOSdata collection
PHASER2.3.0phasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4JR9

4jr9


Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.859 / SU B: 12.544 / SU ML: 0.247 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.54 / ESU R Free: 0.334 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: A strong density on the surface of NarK is likely from the sugar head group of the decylmaltoside detergent used during protein purification and is modelled in the structure as maltose.
RfactorNum. reflection% reflectionSelection details
Rfree0.2686 3642 5 %RANDOM
Rwork0.22337 ---
obs0.22567 68494 94.53 %-
all-72136 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.172 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å2-0.23 Å2-1.11 Å2
2---0.1 Å21.65 Å2
3---0.91 Å2
Refine analyzeLuzzati coordinate error obs: 0.3741 Å
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12522 0 32 35 12589
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212889
X-RAY DIFFRACTIONr_angle_refined_deg1.291.94617560
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.01851646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.01523.137459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.783151921
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5161546
X-RAY DIFFRACTIONr_chiral_restr0.0850.22011
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219620
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 223 -
Rwork0.312 4088 -
obs-4088 77.26 %

+
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