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- PDB-6vbg: Lactose permease complex with thiodigalactoside and nanobody 9043 -

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Basic information

Entry
Database: PDB / ID: 6vbg
TitleLactose permease complex with thiodigalactoside and nanobody 9043
Components
  • Galactoside permease
  • nanobody 9043
KeywordsPROTEIN TRANSPORT / Major Facilitator Superfamily / symport / alternate access conformation change / nanobody binding
Function / homology
Function and homology information


lactose:proton symporter activity / lactose transport / cytidine transmembrane transporter activity / carbohydrate:proton symporter activity / uridine transmembrane transporter activity / lactose binding / : / carbohydrate transport / membrane => GO:0016020 / membrane / plasma membrane
Similarity search - Function
LacY/RafB permease family / LacY/RafB permease family, conserved site / LacY proton/sugar symporter / LacY family proton/sugar symporters signature 1. / LacY family proton/sugar symporters signature 2. / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Galactoside permease / Lactose permease
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsKumar, H. / Stroud, R.M. / Kaback, H.R. / Finer-Moore, J. / Smirnova, I. / Kasho, V. / Pardon, E. / Steyart, J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM24485 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)120043 United States
National Science Foundation (NSF, United States)MCB1747705 United States
Citation
Journal: Plos One / Year: 2020
Title: Diversity in kinetics correlated with structure in nano body-stabilized LacY.
Authors: Kumar, H. / Finer-Moore, J. / Smirnova, I. / Kasho, V. / Pardon, E. / Steyaert, J. / Kaback, H.R. / Stroud, R.M.
#1: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Crystal Structure of a ligand-bound LacY-Nanobody Complex.
Authors: Kumar, H. / Finer-Moore, J.S. / Jiang, X. / Smirnova, I. / Kasho, V. / Pardon, E. / Steyaert, J. / Kaback, H.R. / Stroud, R.M.
History
DepositionDec 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: citation / citation_author / Item: _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galactoside permease
C: nanobody 9043
B: Galactoside permease
D: nanobody 9043
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,95715
Polymers120,4824
Non-polymers3,47411
Water362
1
A: Galactoside permease
C: nanobody 9043
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8257
Polymers60,2412
Non-polymers1,5845
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Galactoside permease
D: nanobody 9043
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1318
Polymers60,2412
Non-polymers1,8906
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)151.270, 151.270, 182.480
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
34
44
54
64
74
84
94

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'A'A1 - 188
121chain 'A'A203 - 408
211(chain 'B' and (resid 1 through 189 or resid 203 through 409))B1 - 188
221(chain 'B' and (resid 1 through 189 or resid 203 through 409))B203 - 408
112(chain 'C' and resid 1 through 117)C1 - 116
212chain 'D'D1 - 116
114chain 'G'G501
214chain 'H'H601
314chain 'I'I701
414chain 'J'J801
514chain 'K'K901
614chain 'L'L501
714chain 'M'M601
814chain 'N'N701
914chain 'O'O801

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein Galactoside permease / Lactose permease / Lactose permease (Lactose-proton symport) / Lactose-proton symport / MFS ...Lactose permease / Lactose permease (Lactose-proton symport) / Lactose-proton symport / MFS transporter / NorA_1_M97169


Mass: 46789.207 Da / Num. of mol.: 2 / Mutation: G46W, G262W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: lacY, lacY_1, lacY_2, lacY_3, A6V01_11495, A8C65_20655, A8M42_15285, ACN68_10080, ACN81_29445, ACU57_18760, AJ318_07830, AKG99_15095, AM270_02570, AM464_18655, AMK83_26120, AML07_16950, AML35_ ...Gene: lacY, lacY_1, lacY_2, lacY_3, A6V01_11495, A8C65_20655, A8M42_15285, ACN68_10080, ACN81_29445, ACU57_18760, AJ318_07830, AKG99_15095, AM270_02570, AM464_18655, AMK83_26120, AML07_16950, AML35_24485, APU18_15875, APZ14_02895, AUQ13_18775, AUS26_08045, AW059_14270, AW106_12030, AWF59_002435, AWG78_006090, AZZ83_000123, B9M99_04475, B9T59_06225, BANRA_00777, BB545_15300, BHF46_20715, BIQ87_01935, BIU72_03550, BK373_01540, BK375_21010, BMT49_03020, BMT91_19335, BOH76_22050, BON66_09310, BON69_11830, BON71_09435, BON92_03420, BON94_14610, BON95_06740, BON96_22525, BUE81_15270, BvCms12BK_03300, BvCms2454_01726, BvCms28BK_00743, BvCmsA75A_04728, BvCmsHHP001_01494, BvCmsHHP019_04502, BvCmsHHP056_04283, BvCmsKKNP011_04619, BvCmsKKP036_04325, BvCmsKSNP019_03228, BvCmsKSNP120_04320, BvCmsKSP015_03661, BvCmsKSP026_02739, BvCmsKSP058_04814, BvCmsKSP083_00737, BvCmsNSNP036_04122, BvCmsNSP006_03638, BvCmsNSP007_00895, BvCmsNSP072_03352, BvCmsSINP011_04898, BvCmsSINP012_01842, BvCmsSIP019_03585, BvCmsSIP044_04786, BVL39_01120, BW690_22770, BWI87_08790, BWI89_12765, BXT93_23905, BZL31_08595, BZL69_13855, C2U48_08360, C3449_08540, C4K41_08290, C5715_13825, C5N07_24640, C5P44_12945, C6669_02995, C6B13_09720, C7235_19125, C7B02_04785, C7B06_24440, C7B07_24140, C7B08_05950, C9025_05365, C9063_01880, C9077_04180, C9078_02330, C9083_15570, C9212_10665, C9E25_04820, C9Y80_12290, C9Y91_05615, C9Y95_06770, C9Z87_09505, CA593_01420, CDL37_09235, CI694_24695, COD30_12260, CQP61_21130, CRD98_01430, CRT46_01825, CSB64_04040, CT143_18850, CT146_24550, CV83915_01231, CWS33_24300, D1912_21130, D2183_00410, D2188_07965, D3821_13115, D3822_04615, D3C88_02070, D3Y67_20835, D6W60_16025, D9D20_17940, D9D33_20360, D9D43_15040, D9F17_03720, D9G48_18410, D9H53_20330, D9H68_14985, D9H70_12020, D9H94_11975, D9I11_08840, D9I20_07450, D9I88_07865, D9I97_15245, D9J11_01945, D9J46_05685, D9J60_08355, D9K48_13755, D9K54_21075, DAH18_14735, DAH32_05885, DAH34_13895, DAH37_22385, DBQ99_19865, DEO04_04305, DIV22_00165, DL800_03635, DM102_12510, DNQ41_05610, DNR41_19640, DNX30_04510, DNX30_30030, DP277_21630, DQF57_07430, DS966_21110, DTL43_07655, DTL90_10485, DTM10_05840, DTM25_14170, DTM45_10720, DU321_19250, DU333_15155, DXT69_23380, DXT73_20905, E2112_14055, E2119_01930, E2127_11985, E2128_04640, E2129_15490, E2134_00125, E2855_00356, E2863_00381, E5P22_06110, E5P37_17460, E5S35_17515, E5S46_09030, E5S47_10100, E5S58_11240, EAI42_17215, EAI46_16235, EAI52_25350, EB575_09280, EC1094V2_3507, EC3234A_4c00200, EC3426_01189, EC382_22725, EC95NR1_04568, ECTO6_03753, ED600_13350, ED648_10345, EIA21_12990, EJH97_18755, EKI52_09385, EL75_3407, EL79_3502, EL80_3454, ELT20_08545, ELT33_21350, ELV05_17125, ELV08_19270, ELV28_08615, EO241_13610, EPS94_20330, EPS97_16790, EPT01_22725, EQ823_11820, EQ825_16155, EQ830_03870, ERS085365_01883, ERS085379_01258, ERS085386_01050, ERS085416_03243, ERS139211_01209, ERS150876_00526, EVY14_07340, EWK56_10075, ExPECSC022_00401, ExPECSC038_04855, EXX06_12625, EXX13_09890, EXX24_01665, EXX55_12100, EXX73_02505, EXX78_04900, EXX87_11790, EYD11_17665, EYX83_13280, FNJ69_23270, FNJ83_03490, FORC28_4807, FORC82_3704, FQ915_24920, FQR64_17860, FQU83_21025, FRV13_03655, FV293_06325, FWK02_14300, GJ11_02155, HmCmsJML079_00608, HmCmsJML122_00139, HmCmsJML146_04035, HmCmsJML204_03576, HMPREF3040_03340, HW43_05365, JD73_11990, MJ49_04715, MS6198_03470, NCTC10082_01120, NCTC10090_01929, NCTC10429_03820, NCTC10766_05668, NCTC13148_06751, NCTC8179_01591, NCTC8959_04986, NCTC8960_01355, NCTC9045_04482, NCTC9050_01807, NCTC9055_00742, NCTC9058_03073, NCTC9062_04425, NCTC9077_04847, NCTC9081_02389, NCTC9111_04021, NCTC9117_04856, NCTC9119_04042, NCTC9703_03267, RG28_03130, RK56_026970, RX35_02023, SAMEA3472055_05173, SAMEA3472056_02980, SAMEA3472080_03897, SAMEA3472090_01855, SAMEA3472110_02233, SAMEA3472112_02272, SAMEA3484427_03921, SAMEA3484429_03823, SAMEA3484434_02913, SAMEA3485101_01840, SAMEA3752372_02293, SAMEA3752557_00172, SAMEA3752559_04815, SAMEA3752620_00744, SAMEA3753164_00177, SAMEA3753300_00417, UC41_01885, UN86_08680, UN91_18970, YDC107_3615
Plasmid: PT7-5 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: C6FW78, UniProt: P02920*PLUS
#2: Antibody nanobody 9043


Mass: 13451.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: PMESY4 / Production host: Escherichia coli (E. coli) / Strain (production host): WK6
#3: Polysaccharide beta-D-galactopyranose-(1-1)-1-thio-beta-D-galactopyranose


Type: oligosaccharide / Mass: 358.362 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/1,2,1/[a2112h-1b_1-5]/1-1/a1-b1*S*WURCSPDB2Glycan 1.1.0
[][b-D-Galp1SH]{[(1+S)][b-D-Galp]{}}LINUCSPDB-CARE
#4: Sugar
ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 5 Å3/Da
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.07 M sodium chloride, 0.05 M sodium citrate pH 4.5,22% v/v PEG 400

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Data collection

DiffractionMean temperature: 103 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 21, 2017
RadiationMonochromator: double flat crystal SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115 Å / Relative weight: 1
ReflectionResolution: 2.8→39.1 Å / Num. obs: 57178 / % possible obs: 98.3 % / Redundancy: 2.899 % / Biso Wilson estimate: 71.73 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.216 / Rrim(I) all: 0.265 / Χ2: 0.802 / Net I/σ(I): 5.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.8-2.92.7612.7240.4557250.1113.34199.2
2.9-32.8212.4150.5150140.1192.96299.4
3-3.52.9141.0581.24173430.4181.30499.4
3.5-42.8940.3363.8997270.8220.41399.1
4-52.910.1219.6795430.9710.14897.9
5-5.53.0560.10211.0624840.9820.12497.6
5.5-63.0060.11110.0417200.9790.13496.9
6-72.8740.08711.9120820.9840.10794.9
7-7.52.9170.06815.346610.9920.08194.3
7.5-83.1580.04422.255260.9960.05395.5
8-103.0510.02730.6211660.9980.03395.4
10-152.8470.02236.958470.9990.02792.3
15-203.190.01845.622110.9990.02291.7
20-303.150.01451.891070.9990.01891.5
30-5030.01257.94220.9990.01653.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6C9W

6c9w


Resolution: 2.8→39.06 Å / SU ML: 0.5568 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.0284
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2748 1976 3.51 %
Rwork0.2389 54354 -
obs0.2401 56330 96.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.9 Å2
Refinement stepCycle: LAST / Resolution: 2.8→39.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8188 0 235 2 8425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00338663
X-RAY DIFFRACTIONf_angle_d0.700411717
X-RAY DIFFRACTIONf_chiral_restr0.0411320
X-RAY DIFFRACTIONf_plane_restr0.00351408
X-RAY DIFFRACTIONf_dihedral_angle_d9.39164825
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.39381240.38253563X-RAY DIFFRACTION89.64
2.87-2.950.38571370.36823692X-RAY DIFFRACTION92.44
2.95-3.030.42441390.37463876X-RAY DIFFRACTION96.84
3.03-3.130.35561450.34493936X-RAY DIFFRACTION98.86
3.13-3.240.33381410.31363979X-RAY DIFFRACTION99.3
3.24-3.370.35951440.28893958X-RAY DIFFRACTION99.11
3.37-3.530.30971470.27893973X-RAY DIFFRACTION98.87
3.53-3.710.31821410.24823972X-RAY DIFFRACTION99.2
3.71-3.950.2521460.22023950X-RAY DIFFRACTION99.15
3.95-4.250.26951380.20673942X-RAY DIFFRACTION98.43
4.25-4.680.22821480.18253903X-RAY DIFFRACTION97.4
4.68-5.350.22111400.18743938X-RAY DIFFRACTION97.84
5.35-6.740.25691470.23723862X-RAY DIFFRACTION96.23
6.74-39.060.23671390.21233810X-RAY DIFFRACTION93.56

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