6VBG

Lactose permease complex with thiodigalactoside and nanobody 9043


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report

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This is version 1.2 of the entry. See complete history


Literature

Diversity in kinetics correlated with structure in nano body-stabilized LacY.

Kumar, H.Finer-Moore, J.Smirnova, I.Kasho, V.Pardon, E.Steyaert, J.Kaback, H.R.Stroud, R.M.

(2020) PLoS One 15: e0232846-e0232846

  • DOI: https://doi.org/10.1371/journal.pone.0232846
  • Primary Citation of Related Structures:  
    6VBG

  • PubMed Abstract: 

    The structure of lactose permease, stabilized in a periplasmic open conformation by two Gly to Trp replacements (LacYww) and complexed with a nanobody directed against this conformation, provides the highest resolution structure of the symporter. The nanobody binds in a different manner than two other nanobodies made against the same mutant, which also bind to the same general region on the periplasmic side. This region of the protein may represent an immune hotspot. The CDR3 loop of the nanobody is held by hydrogen bonds in a conformation that partially blocks access to the substrate-binding site. As a result, kon and koff for galactoside binding to either LacY or the double mutant complexed with the nanobody are lower than for the other two LacY/nanobody complexes though the Kd values are similar, reflecting the fact that the nanobodies rigidify structures along the pathway. While the wild-type LacY/nanobody complex clearly stabilizes a similar 'extracellular open' conformation in solution, judged by binding kinetics, the complex with wild-type LacY did not yet crystallize, suggesting the nanobody does not bind strongly enough to shift the equilibrium to stabilize a periplasmic side-open conformation suitable for crystallization. However, the similarity of the galactoside binding kinetics for the nanobody-bound complexes with wild type LacY and with LacYWW indicates that they have similar structures, showing that the reported co-structures reliably show nanobody interactions with LacY.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, University of California, San Francisco, California, United States of America.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Galactoside permeaseA,
C [auth B]
417Escherichia coliMutation(s): 2 
Gene Names: 
lacYlacY_1lacY_2lacY_3A6V01_11495A8C65_20655A8M42_15285ACN68_10080ACN81_29445ACU57_18760AJ318_07830AKG99_15095AM270_02570AM464_18655AMK83_26120AML07_16950AML35_24485APU18_15875APZ14_02895AUQ13_18775AUS26_08045AW059_14270AW106_12030AWF59_002435AWG78_006090AZZ83_000123B9M99_04475B9T59_06225BANRA_00777BB545_15300BHF46_20715BIQ87_01935BIU72_03550BK373_01540BK375_21010BMT49_03020BMT91_19335BOH76_22050BON66_09310BON69_11830BON71_09435BON92_03420BON94_14610BON95_06740BON96_22525BUE81_15270BvCms12BK_03300BvCms2454_01726BvCms28BK_00743BvCmsA75A_04728BvCmsHHP001_01494BvCmsHHP019_04502BvCmsHHP056_04283BvCmsKKNP011_04619BvCmsKKP036_04325BvCmsKSNP019_03228BvCmsKSNP120_04320BvCmsKSP015_03661BvCmsKSP026_02739BvCmsKSP058_04814BvCmsKSP083_00737BvCmsNSNP036_04122BvCmsNSP006_03638BvCmsNSP007_00895BvCmsNSP072_03352BvCmsSINP011_04898BvCmsSINP012_01842BvCmsSIP019_03585BvCmsSIP044_04786BVL39_01120BW690_22770BWI87_08790BWI89_12765BXT93_23905BZL31_08595BZL69_13855C2U48_08360C3449_08540C4K41_08290C5715_13825C5N07_24640C5P44_12945C6669_02995C6B13_09720C7235_19125C7B02_04785C7B06_24440C7B07_24140C7B08_05950C9025_05365C9063_01880C9077_04180C9078_02330C9083_15570C9212_10665C9E25_04820C9Y80_12290C9Y91_05615C9Y95_06770C9Z87_09505CA593_01420CDL37_09235CI694_24695COD30_12260CQP61_21130CRD98_01430CRT46_01825CSB64_04040CT143_18850CT146_24550CV83915_01231CWS33_24300D1912_21130D2183_00410D2188_07965D3821_13115D3822_04615D3C88_02070D3Y67_20835D6W60_16025D9D20_17940D9D33_20360D9D43_15040D9F17_03720D9G48_18410D9H53_20330D9H68_14985D9H70_12020D9H94_11975D9I11_08840D9I20_07450D9I88_07865D9I97_15245D9J11_01945D9J46_05685D9J60_08355D9K48_13755D9K54_21075DAH18_14735DAH32_05885DAH34_13895DAH37_22385DBQ99_19865DEO04_04305DIV22_00165DL800_03635DM102_12510DNQ41_05610DNR41_19640DNX30_04510DNX30_30030DP277_21630DQF57_07430DS966_21110DTL43_07655DTL90_10485DTM10_05840DTM25_14170DTM45_10720DU321_19250DU333_15155DXT69_23380DXT73_20905E2112_14055E2119_01930E2127_11985E2128_04640E2129_15490E2134_00125E2855_00356E2863_00381E5P22_06110E5P37_17460E5S35_17515E5S46_09030E5S47_10100E5S58_11240EAI42_17215EAI46_16235EAI52_25350EB575_09280EC1094V2_3507EC3234A_4c00200EC3426_01189EC382_22725EC95NR1_04568ECTO6_03753ED600_13350ED648_10345EIA21_12990EJH97_18755EKI52_09385EL75_3407EL79_3502EL80_3454ELT20_08545ELT33_21350ELV05_17125ELV08_19270ELV28_08615EO241_13610EPS94_20330EPS97_16790EPT01_22725EQ823_11820EQ825_16155EQ830_03870ERS085365_01883ERS085379_01258ERS085386_01050ERS085416_03243ERS139211_01209ERS150876_00526EVY14_07340EWK56_10075ExPECSC022_00401ExPECSC038_04855EXX06_12625EXX13_09890EXX24_01665EXX55_12100EXX73_02505EXX78_04900EXX87_11790EYD11_17665EYX83_13280FNJ69_23270FNJ83_03490FORC28_4807FORC82_3704FQ915_24920FQR64_17860FQU83_21025FRV13_03655FV293_06325FWK02_14300GJ11_02155HmCmsJML079_00608HmCmsJML122_00139HmCmsJML146_04035HmCmsJML204_03576HMPREF3040_03340HW43_05365JD73_11990MJ49_04715MS6198_03470NCTC10082_01120NCTC10090_01929NCTC10429_03820NCTC10766_05668NCTC13148_06751NCTC8179_01591NCTC8959_04986NCTC8960_01355NCTC9045_04482NCTC9050_01807NCTC9055_00742NCTC9058_03073NCTC9062_04425NCTC9077_04847NCTC9081_02389NCTC9111_04021NCTC9117_04856NCTC9119_04042NCTC9703_03267RG28_03130RK56_026970RX35_02023SAMEA3472055_05173SAMEA3472056_02980SAMEA3472080_03897SAMEA3472090_01855SAMEA3472110_02233SAMEA3472112_02272SAMEA3484427_03921SAMEA3484429_03823SAMEA3484434_02913SAMEA3485101_01840SAMEA3752372_02293SAMEA3752557_00172SAMEA3752559_04815SAMEA3752620_00744SAMEA3753164_00177SAMEA3753300_00417UC41_01885UN86_08680UN91_18970YDC107_3615

Membrane Entity: Yes 
UniProt
Find proteins for P02920 (Escherichia coli (strain K12))
Explore P02920 
Go to UniProtKB:  P02920
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02920
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
nanobody 9043B [auth C],
D
121Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-galactopyranose-(1-1)-1-thio-beta-D-galactopyranose
E, F
2N/AN/A
Glycosylation Resources
GlyTouCan:  G61532BD
GlyCosmos:  G61532BD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.27α = 90
b = 151.27β = 90
c = 182.48γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Currently 6VBG does not have a validation slider image.



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM24485
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States120043
National Science Foundation (NSF, United States)United StatesMCB1747705

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-25
    Type: Initial release
  • Version 1.1: 2021-06-09
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description