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- PDB-8zxs: Crystal structure of multidrug efflux transporter OqxB from Klebs... -

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Basic information

Entry
Database: PDB / ID: 8zxs
TitleCrystal structure of multidrug efflux transporter OqxB from Klebsiella pneumoniae
ComponentsEfflux pump membrane transporter
KeywordsMEMBRANE PROTEIN / Multidrug efflux transporter / Membrane transporter / Antimicrobial resistance / AMR / Klebsiella pneumoniae / TRANSPORT PROTEIN
Function / homologyHydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein / AcrB/AcrD/AcrF family / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / response to toxic substance / plasma membrane / Efflux pump membrane transporter
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsMurakami, S. / Yamashita, E. / Okada, U.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP21H02412 Japan
Japan Society for the Promotion of Science (JSPS)JP18K06079 Japan
Japan Society for the Promotion of Science (JSPS)21K19337 Japan
CitationJournal: Nat Commun / Year: 2025
Title: Conformational plasticity across phylogenetic clusters of RND multidrug efflux pumps and its impact on substrate specificity.
Authors: Mariya Lazarova / Thomas Eicher / Clara Börnsen / Hui Zeng / Mohd Athar / Ui Okada / Eiki Yamashita / Inga M Spannaus / Max Borgosch / Hi-Jea Cha / Attilio V Vargiu / Satoshi Murakami / Kay ...Authors: Mariya Lazarova / Thomas Eicher / Clara Börnsen / Hui Zeng / Mohd Athar / Ui Okada / Eiki Yamashita / Inga M Spannaus / Max Borgosch / Hi-Jea Cha / Attilio V Vargiu / Satoshi Murakami / Kay Diederichs / Achilleas S Frangakis / Klaas M Pos /
Abstract: Antibiotic efflux plays a key role for the multidrug resistance in Gram-negative bacteria. Multidrug efflux pumps of the resistance nodulation and cell division (RND) superfamily function as part of ...Antibiotic efflux plays a key role for the multidrug resistance in Gram-negative bacteria. Multidrug efflux pumps of the resistance nodulation and cell division (RND) superfamily function as part of cell envelope spanning systems and provide resistance to diverse antibiotics. Here, we identify two phylogenetic clusters of RND proteins with conserved binding pocket residues and show that the transfer of a single conserved residue between both clusters affects the resistance phenotype not only due to changes in the physicochemical properties of the binding pocket, but also due to an altered equilibrium between the conformational states of the transport cycle. We demonstrate, using single-particle cryo-electron microscopy, that AcrB and OqxB, which represent both clusters, adopt fundamentally different apo states, implying distinct mechanisms for initial substrate binding. The observed conformational plasticity appears phylogenetically conserved and likely plays a role in the diversification of the resistance phenotype among homologous RND pumps.
History
DepositionJun 15, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Efflux pump membrane transporter
B: Efflux pump membrane transporter
C: Efflux pump membrane transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)346,33510
Polymers343,1803
Non-polymers3,1567
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25400 Å2
ΔGint-47 kcal/mol
Surface area116070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.392, 165.939, 249.032
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Efflux pump membrane transporter


Mass: 114393.211 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: The 6-His residues are purification tag. / Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: bepE_2, bepE_1, B5L96_27435, GJJ13_005705, GJJ18_08150, NCTC204_03625, NCTC9637_01899, QIG75_20820, SAMEA4364603_03846
Production host: Escherichia coli (E. coli) / References: UniProt: U5U6L7
#2: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H46O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.65 Å3/Da / Density % sol: 66.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 10% PEG 4000, 0.1M ADA, 0.2M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.75→49.34 Å / Num. obs: 130594 / % possible obs: 99.65 % / Redundancy: 7.33 % / Biso Wilson estimate: 93.76 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.032 / Net I/av σ(I): 12.9 / Net I/σ(I): 12.9
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 44929 / CC1/2: 0.498 / % possible all: 95.19

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Cootmodel building
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→43.04 Å / SU ML: 0.4744 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.619
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2877 6532 5.01 %
Rwork0.2363 123910 -
obs0.2389 130442 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 124.68 Å2
Refinement stepCycle: LAST / Resolution: 2.75→43.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23767 0 216 1 23984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00524459
X-RAY DIFFRACTIONf_angle_d0.888233290
X-RAY DIFFRACTIONf_chiral_restr0.05063975
X-RAY DIFFRACTIONf_plane_restr0.00644250
X-RAY DIFFRACTIONf_dihedral_angle_d9.30343421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.780.42182040.40813854X-RAY DIFFRACTION94.44
2.78-2.810.42662140.39864141X-RAY DIFFRACTION99.77
2.81-2.850.3931780.37624095X-RAY DIFFRACTION99.67
2.85-2.880.41622370.37864073X-RAY DIFFRACTION99.65
2.88-2.920.43992110.39724102X-RAY DIFFRACTION99.77
2.92-2.960.43652390.38024133X-RAY DIFFRACTION99.66
2.96-30.37922160.34764011X-RAY DIFFRACTION99.55
3-3.050.39632240.31854094X-RAY DIFFRACTION99.54
3.05-3.10.35872120.29814073X-RAY DIFFRACTION99.58
3.1-3.150.33732110.28254123X-RAY DIFFRACTION99.75
3.15-3.20.33852280.28434108X-RAY DIFFRACTION99.75
3.2-3.260.30292110.26924111X-RAY DIFFRACTION99.84
3.26-3.320.33522090.26854094X-RAY DIFFRACTION99.63
3.32-3.390.32982130.26364121X-RAY DIFFRACTION99.86
3.39-3.460.32342000.26324145X-RAY DIFFRACTION99.93
3.46-3.550.33912330.26024126X-RAY DIFFRACTION99.93
3.55-3.630.31282200.26244095X-RAY DIFFRACTION99.93
3.63-3.730.29862250.24564103X-RAY DIFFRACTION99.93
3.73-3.840.30462050.24084157X-RAY DIFFRACTION99.91
3.84-3.970.28952350.23294122X-RAY DIFFRACTION99.89
3.97-4.110.30012020.23614139X-RAY DIFFRACTION99.75
4.11-4.270.27492010.22564171X-RAY DIFFRACTION99.98
4.27-4.470.25742240.20124167X-RAY DIFFRACTION99.93
4.47-4.70.24232220.19794163X-RAY DIFFRACTION99.91
4.7-4.990.24332050.19414164X-RAY DIFFRACTION100
5-5.380.2882200.21544178X-RAY DIFFRACTION99.98
5.38-5.920.26522510.2374177X-RAY DIFFRACTION99.98
5.92-6.770.28742250.24064230X-RAY DIFFRACTION99.96
6.77-8.520.24282160.19584257X-RAY DIFFRACTION99.58
8.52-43.040.27082410.22454383X-RAY DIFFRACTION98.97
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)
10.6395754282410.1288077444940.1194671976150.5415926628440.2372430155450.818263737553-0.106663929338-0.125933737478-0.1384913239520.2981915542630.0451570063841-0.05474877763140.450587604476-0.0657560658407-5.87908983635E-50.823807568720.03585398727690.1663082124060.7714927689060.03121660423750.848566149338-1.39904292126-2.09509218996-12.3515843074
20.7051715213-0.07171783268540.0143402284724-0.0232081381111-0.3050925518491.169062366480.1112461342290.066717559154-0.004723392087110.00878721784486-0.0469443728668-0.02304871511260.411651105284-0.528288007648-0.001857335537590.725396961609-0.2544694522720.04876278258620.946405871456-0.245240622230.812030923638-14.4054059027-13.122491993-41.571162953
31.11038114118-0.659427556529-0.7667456845191.474650735640.4554833336250.973253450319-0.0701369091749-0.2149034311750.02398538411080.0960824845429-0.1751585687520.1848952941080.0211184695308-0.665191061644-0.00179095718450.6012940353950.03190968729870.009871570271540.991807567626-0.0139894987210.709216636059-12.735104560420.5897888084-7.55551067071
40.848114725186-0.3802261057630.1605957312420.961844577553-0.888887628630.8335254185950.02845397441940.106830031793-0.0133162377396-0.346754374824-0.2740247142730.1599230769250.592941354932-0.487101173885-0.001448078498980.9074985593680.2875228470450.006104523288151.50025525694-0.09031547196920.974114143632-9.6932087983724.2092975919-24.455981561
50.500181851146-0.2589498009080.606359486341.14019054973-0.6831380930190.803019998772-0.2640568266030.551147336607-0.356096840256-0.09339458522830.365213154710.3473845140770.486238654452-0.684321032194-1.45113724533E-60.831925526491-0.1501171525430.09908230091871.19537901175-0.2975473579461.04567127669-12.1199071951-13.1769123241-57.3320488324
61.99011685521-0.2710603408680.06304266825310.357286287412-0.1031698465751.48282509890.149187764581-0.367443042283-0.1491987036190.3088406733640.05943375350770.07665766612820.497231203932-0.3118548987310.03347078210950.9287667695590.076043310017-0.1543784855050.4740782427620.1389045845520.68397040441926.8673196182-5.49105305325-9.67386530346
70.812828539445-0.6719075448450.2372789619691.12052429984-0.4595569770490.235039133654-0.0995300182853-0.2802678858170.06101140527940.007028073630630.1038992206-0.386794629880.1917931344710.514881214911-7.6047931028E-51.014607371340.0988785546666-0.07374816432031.263743854260.01816879743340.902089658736.160001803723.05663718258.17187015507
81.04520437546-0.345027356722-0.8253866540930.07988194078460.2399718557570.7385468094510.4754940618770.438949269591-0.534056932222-0.357679471049-0.064519404815-0.3464665630530.4336430243830.879495063029-0.05069477771591.680868650050.599270232877-0.2676640933041.19208122417-0.04892114895041.1137181803245.035472127-14.7665346944-10.544942542
90.3536362272160.0814105400206-0.06139792332780.01810248409090.09806802734050.1936324110390.1661455987780.31665047161-0.400025606656-0.3569811261240.03801396297290.1024906054310.2992608632350.5159656231670.1122416556871.957720502010.565505074663-0.1324168047930.955595363229-0.30320933381.2016595913335.5443071548-39.4027915138-36.5758688429
101.72512882863-1.51125999642-1.035027353581.706753464390.5918063177880.961010834054-0.198593913635-1.401377160720.8598896248190.7875650536020.601244177382-0.460228979670.3186871273730.4308473913831.985605815391.479257635660.470903754726-0.2077579637460.7417618097740.5775195837260.42599125190530.448836357-26.8703525661.54403985003
110.02166096189410.1103171224330.1368850118970.4939711456970.6354659749760.7936285540520.2886296623190.614198192671-0.693168050483-0.0934262018127-0.7198953665080.1430098231110.561877262815-0.108939160931-0.02498190800681.684178721750.516183532244-0.2154861430931.267574297040.1760128342481.1555268025937.6032958529-23.97319399336.25873571574
120.1244298735450.090670578294-0.5249436634180.549110069326-0.563358182472.09727508787-0.085141168141-0.020291798368-0.1950204336570.09838358172350.1836819610730.09500651163570.792585609795-0.295516911429-0.002752930653061.38558411387-0.0235251693046-0.0566334291851.267507409170.1345391602231.040087355320.75794941472.974077787320.8094518234
130.2078013342310.2810293607450.4399281477760.3582994209850.5741210943770.5811416939580.744039582048-0.338375559805-0.1560101953820.567864631605-0.585141859038-0.3145864945450.703203052055-0.808794768797-0.0277410438841.60155477104-0.168590747375-0.1236134422770.9077553920130.08959441993650.73889695220312.1972777013-24.7733299905-4.3902403702
141.399458083820.597054817112-0.2825067079580.243444132894-0.04893607810570.4192890157150.418068894458-0.179528198657-1.07639537443-0.1196383451-0.373788532121-0.0181890055756-0.264994419588-0.3084640996580.02568467151142.613913963740.304128663724-0.2892599211720.929022873971-0.2932901993221.7519939523725.0138069172-47.5378954603-27.7766241129
150.5694416295430.402361585916-0.1684624571290.4045410824740.1262255750621.136947365710.328012964682-0.11825775625-0.1036617207910.719910995819-0.110256376086-0.2069603543170.692813188160.203461848741-0.005881030423860.6389948922950.05703512877940.05011655011370.738830405469-0.1224632877240.77287439101926.15568934586.66872894595-33.5725718307
160.199599191615-0.06209074320780.077692549550.2991657554730.166860146240.2555314823430.0400239154812-0.11698221502-0.2075286307540.2179401132760.139116716344-0.0372278245976-0.372816952377-0.606804738032-0.001414067261560.9193011759970.09907038484360.1098636174121.12974402825-0.1100408774790.86026396544721.184378617223.7185496573-20.4479290754
170.125740095838-0.112902880272-0.1353556689640.1198193170640.01463534812010.222215349534-0.1171363125-0.06754604370540.1714678376210.0742454609887-0.1692696160940.0125197111269-0.08974259694630.0256930141275-0.0001384595119090.6802440666270.02313919108610.012664929781.04128540875-0.1333369381390.8215038642177.068549975334.918144431-6.47421516438
180.1922233113570.142685969966-0.3962049499880.276192604602-0.1199641757540.560705107078-0.007257684432550.7316015661970.130934073508-0.244035577328-0.112022423159-0.07222479046940.0687520410343-0.3372806298633.91444848978E-50.720259114464-0.01220578441520.003196804925641.15500403389-0.1752566701521.0562269320815.883352147637.6700386465-23.7231142084
190.7709672497050.03010906367370.2280103097280.274122747761-0.00359008216121.833661401290.05774345255150.330769592088-0.0773631294113-0.0867943142462-0.0122471061168-0.09626281832810.2460426130190.6272801168950.0004724287159340.962213186590.1250134392890.03048774907491.23246955843-0.1325324269830.83437443890131.89528884095.61956016082-59.7973242798
200.549548687880.1965492946450.4112845363171.193040028850.5546522683160.620489601346-0.1743547943680.05896659910640.100203319685-0.1406202865180.08467290667560.03211271594370.04145584886840.531504623363-5.28311109293E-50.771784637899-0.0869373868298-0.03428504273661.16258732058-0.005911676612490.93461902656837.275446224133.2711849061-16.8934248153
210.4821236340740.4249072931650.4592661527810.5218779041750.629355787442.6376064794-0.0844381410787-0.132994290840.399612541552-0.03113490695870.416364278497-0.51910865102-0.2868829147811.96314541212-0.6098478362540.5009970441560.2909849564830.03763593044591.82526494048-0.2321043434530.76069062117647.90858119686.20102192883-38.456648953
220.537212259387-0.05894906112640.05553599107850.00349787391722-0.02569688370820.8389718998640.0589389171490.2370413222430.1273625554670.0648389643580.246603963357-0.4144394578760.1258835858141.01008427823-0.0822717002890.7277812491350.2430592129980.03257083858641.73075023725-0.4378196518810.77867412947643.5952222313-5.5439400864-63.7369016777
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 426 )AA1 - 4261 - 426
22chain 'A' and (resid 427 through 631 )AA427 - 631427 - 631
33chain 'A' and (resid 632 through 801 )AA632 - 801632 - 801
44chain 'A' and (resid 802 through 877 )AA802 - 877802 - 877
55chain 'A' and (resid 878 through 1040 )AA878 - 1040878 - 1040
66chain 'B' and (resid 1 through 163 )BB1 - 1631 - 163
77chain 'B' and (resid 164 through 275 )BB164 - 275164 - 275
88chain 'B' and (resid 276 through 361 )BB276 - 361276 - 361
99chain 'B' and (resid 362 through 542 )BB362 - 542362 - 542
1010chain 'B' and (resid 543 through 631 )BB543 - 631543 - 631
1111chain 'B' and (resid 632 through 684 )BB632 - 684632 - 684
1212chain 'B' and (resid 685 through 816 )BB685 - 816685 - 816
1313chain 'B' and (resid 817 through 898 )BB817 - 898817 - 898
1414chain 'B' and (resid 899 through 1042 )BB899 - 1042899 - 1042
1515chain 'C' and (resid 1 through 101 )CC1 - 1011 - 101
1616chain 'C' and (resid 102 through 163 )CC102 - 163102 - 163
1717chain 'C' and (resid 164 through 250 )CC164 - 250164 - 250
1818chain 'C' and (resid 251 through 331 )CC251 - 331251 - 331
1919chain 'C' and (resid 332 through 631 )CC332 - 631332 - 631
2020chain 'C' and (resid 632 through 833 )CC632 - 833632 - 833
2121chain 'C' and (resid 834 through 898 )CC834 - 898834 - 898
2222chain 'C' and (resid 899 through 1041 )CC899 - 1041899 - 1041

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