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- PDB-6wvd: Human JAGN1 -

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Basic information

Entry
Database: PDB / ID: 6wvd
TitleHuman JAGN1
ComponentsGreen fluorescent protein, Protein jagunal homolog 1 chimera
KeywordsMEMBRANE PROTEIN / JAGN1 / Protein jagunal homolog 1
Function / homology
Function and homology information


: / granulocyte colony-stimulating factor signaling pathway / neutrophil differentiation / neutrophil migration / neutrophil mediated immunity / endoplasmic reticulum organization / negative regulation of insulin secretion involved in cellular response to glucose stimulus / exocytosis / defense response to fungus / vesicle-mediated transport ...: / granulocyte colony-stimulating factor signaling pathway / neutrophil differentiation / neutrophil migration / neutrophil mediated immunity / endoplasmic reticulum organization / negative regulation of insulin secretion involved in cellular response to glucose stimulus / exocytosis / defense response to fungus / vesicle-mediated transport / bioluminescence / generation of precursor metabolites and energy / protein transport / membrane => GO:0016020 / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Protein jagunal / Jagunal, ER re-organisation during oogenesis / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Green fluorescent protein / Protein jagunal homolog 1
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsYang, Y. / Liu, S. / Li, W.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01 HL121718 United States
Other privateForefront of Science Award United States
Other privateMCII 2020-854 United States
National Institutes of Health/National Eye Institute (NIH/NEI)R21 EY028705 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM131008 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM124165 United States
CitationJournal: Sci Adv / Year: 2020
Title: Termini restraining of small membrane proteins enables structure determination at near-atomic resolution.
Authors: Liu, S. / Li, S. / Yang, Y. / Li, W.
History
DepositionMay 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein, Protein jagunal homolog 1 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9033
Polymers48,1901
Non-polymers7132
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.774, 42.718, 111.782
Angle α, β, γ (deg.)90.000, 103.790, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Green fluorescent protein, Protein jagunal homolog 1 chimera


Mass: 48190.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Homo sapiens (human)
Gene: GFP, JAGN1 / Production host: Komagataella pastoris (fungus) / References: UniProt: P42212, UniProt: Q8N5M9
#2: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.18 Å3/Da / Density % sol: 43.51 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase
Details: 30% PEG400, 0.1 M Li2SO4, 0.1M NaCl, 0.1 M Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 19195 / % possible obs: 95.6 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.062 / Rrim(I) all: 0.11 / Χ2: 1.108 / Net I/σ(I): 8.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.292.70.6078980.6250.4180.7411.00893.3
2.29-2.332.70.4989120.7260.3480.611.00895.1
2.33-2.382.80.4039730.8010.2820.4941.03295.7
2.38-2.422.70.389110.8330.2660.4661.04596.8
2.42-2.482.70.3239500.8570.230.3981.10295.8
2.48-2.532.60.2939050.8740.2120.3641.09293.3
2.53-2.62.70.269540.9060.180.3181.20895.5
2.6-2.672.90.2199200.9360.1480.2651.15195.4
2.67-2.752.90.1949480.9490.1310.2361.15896.9
2.75-2.832.90.1819510.9550.1220.2191.23696.5
2.83-2.942.90.159500.9680.1010.1811.17497
2.94-3.052.80.1329460.9730.0910.1611.19195.7
3.05-3.192.70.119030.9770.0780.1361.14792.6
3.19-3.3630.0999630.9810.0670.121.11797.2
3.36-3.5730.0929630.9830.0620.1121.196
3.57-3.852.90.089660.9880.0540.0971.09396.2
3.85-4.232.80.0729190.9880.050.0881.09193.6
4.23-4.8530.0619680.9920.0410.0741.01297.4
4.85-6.12.90.0629660.990.0430.0761.15895.1
6.1-502.90.05610090.9930.0370.0681.02396

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3P

2b3p


Resolution: 2.25→38.44 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2272 922 4.8 %
Rwork0.195 18273 -
obs0.1965 19195 95.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.44 Å2 / Biso mean: 44.6338 Å2 / Biso min: 20.13 Å2
Refinement stepCycle: final / Resolution: 2.25→38.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3204 0 25 95 3324
Biso mean--52.81 45.57 -
Num. residues----398
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.370.27941320.23252550268295
2.37-2.520.26811350.21742614274996
2.52-2.710.25571350.20752546268195
2.71-2.980.2641200.21452628274897
2.98-3.420.26391210.20052610273195
3.42-4.30.20571220.17942636275895
4.3-38.440.19481570.18392689284696
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.65370.48571.25093.1252.23114.015-0.1505-0.01940.1332-0.2833-0.25820.3213-0.3746-0.30030.38990.30560.0182-0.02260.2014-0.00610.3226-4.5112-5.495240.9419
22.55860.6423-1.61251.7662-0.38916.88170.09350.31620.1981-0.0821-0.0254-0.1055-0.4971-0.5089-0.11670.20290.03670.01890.2340.00430.317330.6341-2.39983.4029
33.85660.3238-3.65060.152-0.60533.6844-0.070.1163-0.0772-0.0259-0.06110.03360.2103-0.15910.10670.2425-0.03520.01980.2448-0.03310.250228.8054-11.84586.528
42.8538-0.57620.12522.57730.71833.3243-0.1203-0.0472-0.0236-0.0311-0.07310.06810.0411-0.17060.19580.27910.011-0.01930.22760.0240.2046-0.5106-10.847839.9461
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 163 )A1 - 163
2X-RAY DIFFRACTION2chain 'A' and (resid 164 through 236 )A164 - 236
3X-RAY DIFFRACTION3chain 'A' and (resid 237 through 337 )A237 - 337
4X-RAY DIFFRACTION4chain 'A' and (resid 338 through 413 )A338 - 413

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