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- PDB-6sln: Structure of the RagAB peptide transporter -

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Basic information

Entry
Database: PDB / ID: 6sln
TitleStructure of the RagAB peptide transporter
Components
  • GLN-THR-ALA-GLY-ALA-ASN-SER-GLN-ARG-GLY-SER-ALA-GLY
  • Lipoprotein RagB
  • RagA protein
KeywordsMEMBRANE PROTEIN / outer membrane protein / Bacteroidetes / TonB dependent transporter
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
CarboxypepD_reg-like domain / TonB-dependent outer membrane protein, SusC/RagA / TonB-dependent outer membrane protein SusC/RagA, conserved site / SusD-like, N-terminal / Starch-binding associating with outer membrane / RagB/SusD domain / SusD family / Carboxypeptidase-like, regulatory domain superfamily / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel ...CarboxypepD_reg-like domain / TonB-dependent outer membrane protein, SusC/RagA / TonB-dependent outer membrane protein SusC/RagA, conserved site / SusD-like, N-terminal / Starch-binding associating with outer membrane / RagB/SusD domain / SusD family / Carboxypeptidase-like, regulatory domain superfamily / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain / TonB-dependent receptor-like, beta-barrel domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / PALMITIC ACID / Lipoprotein RagB / RagA protein
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
Porphyromonas gingivalis W83 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsMadej, M. / Ranson, N.A. / White, J.B.R.
CitationJournal: Nat Microbiol / Year: 2020
Title: Structural and functional insights into oligopeptide acquisition by the RagAB transporter from Porphyromonas gingivalis.
Authors: Mariusz Madej / Joshua B R White / Zuzanna Nowakowska / Shaun Rawson / Carsten Scavenius / Jan J Enghild / Grzegorz P Bereta / Karunakar Pothula / Ulrich Kleinekathoefer / Arnaud Baslé / ...Authors: Mariusz Madej / Joshua B R White / Zuzanna Nowakowska / Shaun Rawson / Carsten Scavenius / Jan J Enghild / Grzegorz P Bereta / Karunakar Pothula / Ulrich Kleinekathoefer / Arnaud Baslé / Neil A Ranson / Jan Potempa / Bert van den Berg /
Abstract: Porphyromonas gingivalis, an asaccharolytic member of the Bacteroidetes, is a keystone pathogen in human periodontitis that may also contribute to the development of other chronic inflammatory ...Porphyromonas gingivalis, an asaccharolytic member of the Bacteroidetes, is a keystone pathogen in human periodontitis that may also contribute to the development of other chronic inflammatory diseases. P. gingivalis utilizes protease-generated peptides derived from extracellular proteins for growth, but how these peptides enter the cell is not clear. Here, we identify RagAB as the outer-membrane importer for these peptides. X-ray crystal structures show that the transporter forms a dimeric RagAB complex, with the RagB substrate-binding surface-anchored lipoprotein forming a closed lid on the RagA TonB-dependent transporter. Cryo-electron microscopy structures reveal the opening of the RagB lid and thus provide direct evidence for a 'pedal bin' mechanism of nutrient uptake. Together with mutagenesis, peptide-binding studies and RagAB peptidomics, our work identifies RagAB as a dynamic, selective outer-membrane oligopeptide-acquisition machine that is essential for the efficient utilization of proteinaceous nutrients by P. gingivalis.
History
DepositionAug 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RagA protein
B: RagA protein
C: Lipoprotein RagB
D: Lipoprotein RagB
P: GLN-THR-ALA-GLY-ALA-ASN-SER-GLN-ARG-GLY-SER-ALA-GLY
Q: GLN-THR-ALA-GLY-ALA-ASN-SER-GLN-ARG-GLY-SER-ALA-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)338,22517
Polymers333,2546
Non-polymers4,97111
Water9,404522
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33510 Å2
ΔGint-115 kcal/mol
Surface area97800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.781, 142.734, 250.048
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

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Protein , 2 types, 4 molecules ABCD

#1: Protein RagA protein


Mass: 110162.195 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Porphyromonas gingivalis (strain ATCC BAA-308 / W83) (bacteria)
Strain: ATCC BAA-308 / W83 / References: UniProt: Q7MXJ7
#2: Protein Lipoprotein RagB


Mass: 55259.734 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Porphyromonas gingivalis (strain ATCC BAA-308 / W83) (bacteria)
Strain: ATCC BAA-308 / W83 / References: UniProt: F5H948

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Protein/peptide / Sugars , 2 types, 6 molecules PQ

#3: Protein/peptide GLN-THR-ALA-GLY-ALA-ASN-SER-GLN-ARG-GLY-SER-ALA-GLY


Mass: 1205.218 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Porphyromonas gingivalis W83 (bacteria)
#5: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 4 types, 529 molecules

#4: Chemical ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#6: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#7: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 522 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.71 Å3/Da / Density % sol: 66.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.5
Details: 15% PEG1000 0.05 M Li-sulphate 0.05 M Na-phosphate monobasic 0.08 M Na-citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.917 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 2.61→142.7 Å / Num. obs: 141223 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 43.15 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.102 / Rrim(I) all: 0.278 / Net I/σ(I): 5.6
Reflection shellResolution: 2.61→2.65 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 6762 / CC1/2: 0.53 / Rpim(I) all: 0.752 / Rrim(I) all: 2.079

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PHENIX1.15.2_3472refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SLI

6sli


Resolution: 2.61→123.96 Å / SU ML: 0.4013 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.9094
RfactorNum. reflection% reflection
Rfree0.2642 6888 4.89 %
Rwork0.2067 --
obs0.2096 140898 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 54.61 Å2
Refinement stepCycle: LAST / Resolution: 2.61→123.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21974 0 277 522 22773
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007922745
X-RAY DIFFRACTIONf_angle_d1.024630746
X-RAY DIFFRACTIONf_chiral_restr0.05343268
X-RAY DIFFRACTIONf_plane_restr0.00574001
X-RAY DIFFRACTIONf_dihedral_angle_d6.456113463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.640.39052070.33284222X-RAY DIFFRACTION94.8
2.64-2.670.39872150.31664384X-RAY DIFFRACTION99.67
2.67-2.70.37232250.29924441X-RAY DIFFRACTION99.76
2.7-2.740.32832140.27994426X-RAY DIFFRACTION99.78
2.74-2.770.37012420.28094427X-RAY DIFFRACTION99.79
2.77-2.810.35892290.26814426X-RAY DIFFRACTION99.87
2.81-2.850.32412240.26164458X-RAY DIFFRACTION99.83
2.85-2.890.33512160.2544420X-RAY DIFFRACTION99.87
2.89-2.940.32522300.26014457X-RAY DIFFRACTION99.87
2.94-2.990.32852410.26274404X-RAY DIFFRACTION99.87
2.99-3.040.30352200.26744454X-RAY DIFFRACTION99.83
3.04-3.090.34222050.25934482X-RAY DIFFRACTION99.72
3.09-3.150.32112360.24314415X-RAY DIFFRACTION99.91
3.15-3.220.32432170.24114474X-RAY DIFFRACTION99.89
3.22-3.290.32342220.23044452X-RAY DIFFRACTION99.98
3.29-3.360.29382360.21074437X-RAY DIFFRACTION99.96
3.36-3.450.27972230.20814463X-RAY DIFFRACTION99.94
3.45-3.540.2672730.19964409X-RAY DIFFRACTION99.87
3.54-3.650.26352100.1984517X-RAY DIFFRACTION99.87
3.65-3.760.28562260.20644464X-RAY DIFFRACTION99.91
3.76-3.90.28442250.19364476X-RAY DIFFRACTION99.98
3.9-4.050.24142200.18364504X-RAY DIFFRACTION99.98
4.05-4.240.21862430.17824470X-RAY DIFFRACTION99.98
4.24-4.460.22462570.16294489X-RAY DIFFRACTION99.96
4.46-4.740.19842380.15014491X-RAY DIFFRACTION100
4.74-5.110.20632380.154529X-RAY DIFFRACTION99.98
5.11-5.620.20362180.15574541X-RAY DIFFRACTION100
5.62-6.440.20632500.16494562X-RAY DIFFRACTION99.92
6.44-8.110.21332230.174608X-RAY DIFFRACTION99.88
8.11-123.960.23612650.22914708X-RAY DIFFRACTION98.61
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)
10.742057665710.0170568543444-0.05140610668130.6212906658430.04013465691310.260453982058-0.01417104842120.219789714217-0.324856892839-0.1768345750780.0164277012940.01727822263730.122944454118-0.005522754165370.006865320482620.370044233869-0.00310054226258-0.02087123757010.366664799668-0.09818829442360.520095637189-32.9878942688-18.081699547239.5747267145
20.686882933474-0.03432425665620.07691099139940.611828196967-0.03062966587620.279537707193-0.001692646783860.1540740659390.268800026657-0.184627829915-0.01601159702050.062350093964-0.116270283189-0.01954766073130.02421340974640.3854128361930.000180168063853-0.01005543768640.3540119213470.086597154020.521028526855-32.309524416535.124981355942.6496859605
30.775078458751-0.07054878943870.1710167356310.8383743790940.04901211270030.664878396904-0.00594990170626-0.1826037108330.1906789663340.209027045813-0.006255616775330.139308018443-0.0865368632097-0.07732900828410.008902360902390.3365040398050.006670492784820.07341495371060.337702266172-0.07792661861060.419900441141-40.972729208132.079451668585.0619249777
40.8362201447360.229522273975-0.1001200420350.983250598836-0.09024537600510.6413999107940.0187311719232-0.190799393724-0.3508276859770.168532878539-0.0510203777438-0.04651774395210.1030470039190.06742853232260.02045657469290.3602203072780.0164880337445-0.03112936673220.3712486101010.1208549405980.520263945112-23.8816392944-19.913925070581.8802831872
50.00845274978921-0.054415655710.02584001930660.380651453472-0.1822470168970.088914882672-0.2177155731760.4091195382830.418480286125-0.2083556385520.008530771923370.113393910723-0.4138500759420.2518363967050.2170289008580.746483427982-0.06304849083930.01351910704290.7980362417680.0955588149351.02055505125-32.812493161440.314321580760.0871653129
60.01361320477430.002088546629380.009848202644270.038144402804-0.01745369182180.01678243763560.02232608983170.01062858565270.0534956527864-0.00290657086443-0.05550071178270.013423656307-0.0639638144529-0.02724176204910.002855495158260.498678520063-0.167181214175-0.03898381693220.597334072376-0.01252987740440.714823914762-32.6482213213-25.313350467655.7427439489
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 115 through 1017)
2X-RAY DIFFRACTION2(chain 'B' and resid 115 through 1017)
3X-RAY DIFFRACTION3(chain 'C' and resid 20 through 500)
4X-RAY DIFFRACTION4(chain 'D' and resid 20 through 501)
5X-RAY DIFFRACTION5(chain 'P' and resid 2 through 14)
6X-RAY DIFFRACTION6(chain 'Q' and resid 2 through 14)

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