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

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Basic information

Entry
Database: PDB / ID: 6slj
TitleStructure of the RagAB peptide transporter
Components
  • (ALA-SER-THR-THR-GLY-ALA-ASN-SER-GLN- ...) x 2
  • 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: 3.04 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 / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)338,20617
Polymers333,0316
Non-polymers5,17511
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33170 Å2
ΔGint-98 kcal/mol
Surface area99860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.597, 142.021, 241.590
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUVALVAL(chain 'A' and (resid 115 through 721 or resid 723...AB115 - 72095 - 700
121TYRTYRTHRTHR(chain 'A' and (resid 115 through 721 or resid 723...AB723 - 726703 - 706
131ASPASPGLNGLN(chain 'A' and (resid 115 through 721 or resid 723...AB729 - 835709 - 815
141LYSLYSGLUGLU(chain 'A' and (resid 115 through 721 or resid 723...AB842 - 853822 - 833
151ILEILEPHEPHE(chain 'A' and (resid 115 through 721 or resid 723...AB856 - 1017836 - 997
261LEULEUVALVAL(chain 'B' and (resid 115 through 721 or resid 723...BA115 - 72095 - 700
271TYRTYRTHRTHR(chain 'B' and (resid 115 through 721 or resid 723...BA723 - 726703 - 706
281ASPASPGLNGLN(chain 'B' and (resid 115 through 721 or resid 723...BA729 - 835709 - 815
291LYSLYSGLUGLU(chain 'B' and (resid 115 through 721 or resid 723...BA842 - 853822 - 833
2101ILEILEPHEPHE(chain 'B' and (resid 115 through 721 or resid 723...BA856 - 1017836 - 997
1112CYSCYSPROPROchain 'C'CC20 - 5001 - 481
2122CYSCYSPROPROchain 'D'DD20 - 5001 - 481

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules BACD

#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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ALA-SER-THR-THR-GLY-ALA-ASN-SER-GLN- ... , 2 types, 2 molecules PQ

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


Mass: 1194.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis W83 (bacteria)
#4: Protein/peptide ALA-SER-THR-THR-GLY-ALA-ASN-SER-GLN-ARG


Mass: 993.011 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis W83 (bacteria)

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Sugars , 1 types, 5 molecules

#7: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 3 types, 6 molecules

#5: 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.: 2 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#8: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2

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Details

Has ligand of interestN
Has protein modificationY

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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: 3.6 Å3/Da / Density % sol: 65.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.5 / Details: 22% PEG400 0.07 M NaCl 0.05 M Na-citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.04→80.53 Å / Num. obs: 87154 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 45.05 Å2 / CC1/2: 0.95 / Rpim(I) all: 0.157 / Rrim(I) all: 0.43 / Net I/σ(I): 3.7
Reflection shellResolution: 3.04→3.09 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4279 / CC1/2: 0.671 / Rpim(I) all: 0.558 / Rrim(I) all: 1.551

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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: 3.04→71.01 Å / SU ML: 0.4897 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.3961
RfactorNum. reflection% reflection
Rfree0.2952 4346 5 %
Rwork0.2217 --
obs0.2254 86883 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 41.91 Å2
Refinement stepCycle: LAST / Resolution: 3.04→71.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21917 0 241 0 22158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010422672
X-RAY DIFFRACTIONf_angle_d1.299930641
X-RAY DIFFRACTIONf_chiral_restr0.06913248
X-RAY DIFFRACTIONf_plane_restr0.0083990
X-RAY DIFFRACTIONf_dihedral_angle_d6.533415077
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.04-3.070.36351410.29522662X-RAY DIFFRACTION99.15
3.07-3.110.36331560.28472750X-RAY DIFFRACTION99.76
3.11-3.150.33671560.2832665X-RAY DIFFRACTION99.79
3.15-3.190.37881560.28272729X-RAY DIFFRACTION99.35
3.19-3.230.34111480.26642714X-RAY DIFFRACTION99.86
3.23-3.270.3441600.27822700X-RAY DIFFRACTION99.9
3.27-3.320.35431480.26192708X-RAY DIFFRACTION99.79
3.32-3.370.36991210.25412738X-RAY DIFFRACTION100
3.37-3.420.35751520.25412737X-RAY DIFFRACTION99.9
3.42-3.480.35991460.25382701X-RAY DIFFRACTION99.75
3.48-3.540.30581550.23682743X-RAY DIFFRACTION99.9
3.54-3.60.34531350.23892727X-RAY DIFFRACTION99.97
3.6-3.670.31071540.22482717X-RAY DIFFRACTION99.93
3.67-3.750.30671330.21622749X-RAY DIFFRACTION99.93
3.75-3.830.2891560.21352744X-RAY DIFFRACTION99.9
3.83-3.920.29681450.212734X-RAY DIFFRACTION99.76
3.92-4.020.25681290.20632754X-RAY DIFFRACTION99.83
4.02-4.120.26921300.20332766X-RAY DIFFRACTION99.93
4.12-4.250.31911270.20292746X-RAY DIFFRACTION99.9
4.25-4.380.2191240.18952796X-RAY DIFFRACTION99.86
4.38-4.540.27671490.17882727X-RAY DIFFRACTION100
4.54-4.720.22771390.17162783X-RAY DIFFRACTION99.97
4.72-4.940.23941460.18082756X-RAY DIFFRACTION99.9
4.94-5.20.26091440.18532772X-RAY DIFFRACTION99.93
5.2-5.520.25911490.1952776X-RAY DIFFRACTION99.93
5.52-5.950.27621510.19432789X-RAY DIFFRACTION99.9
5.95-6.550.31311440.20262780X-RAY DIFFRACTION99.83
6.55-7.490.23661510.19632809X-RAY DIFFRACTION99.76
7.49-9.440.24441600.19462844X-RAY DIFFRACTION99.87
9.44-71.010.32561410.29412921X-RAY DIFFRACTION97.55
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)
10.8392815177360.0388383706282-0.2206473165530.958077025358-0.01328162350580.159593615177-0.02194009914430.188241261845-0.140735011624-0.19165047557-0.0207014062407-0.04376187141920.0829454318783-0.04023387952970.05169015804440.253583338556-0.010165399308-0.01548750870050.28502667372-0.04438272216110.29928521456432.412049106933.782015782440.3536428838
20.718548531179-0.01877915155260.04830945041210.559586155736-0.1174290219680.352649438445-0.003188005565180.1818463373880.255816503576-0.1487150423160.010329905603-0.0238830189137-0.09650096851880.0176138446784-0.004392310265510.2465290839240.003028559364170.01713300050980.2594566779890.05072495486960.35904203445333.30517627286.734687361737.7680160112
30.7569383757440.425406279260.1296012172880.944971605213-0.1027754900630.5897656865360.0610499907534-0.175154630780.2398500246590.199050006875-0.03169170884430.134698934293-0.117370302997-0.090428648732-0.03802403867490.2575395608670.03359712438870.06076832188780.287180259763-0.08257897939320.35772027944124.361862857688.475290068280.4080139009
40.9548709645080.376124675267-0.3418575960641.023231755110.07271680465660.5458742524950.0135754807464-0.133625064016-0.05539673344640.180552733352-0.0173460744684-0.07598705631990.03661541329680.0296222234763-0.001822869462260.2130286993750.0136809666159-0.0410765373940.2479432357320.0301755958970.21929802839540.932218590436.250672854182.9988991526
56.3115968162-2.0858494236-0.7580407590633.733599862221.282336920640.6475491675040.1934845042640.4572909337220.665941635716-0.4615079270510.0496784560531-0.497342260604-0.2506440058020.0683215384233-0.2534299548280.595701882587-0.2006387197690.008063626981630.6523747003030.1467973211730.76158194921431.494276423128.646943807758.9091718796
61.87950607251-1.215037306981.70316335621.13091098662-2.136315106144.639948807010.367178073382-0.560580928426-0.656158114815-0.0258265202050.008726323946540.1372029089560.340126530309-0.479952032212-0.3979845969520.537725595359-0.123784113487-0.01856301981080.6835944291490.04146272875140.74474437686535.300604748994.195985112857.7065421865
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'B' and resid 115 through 1017)
2X-RAY DIFFRACTION2(chain 'A' and resid 115 through 1017)
3X-RAY DIFFRACTION3(chain 'C' and resid 20 through 501)
4X-RAY DIFFRACTION4(chain 'D' and resid 20 through 501)
5X-RAY DIFFRACTION5(chain 'P' and resid 1 through 13)
6X-RAY DIFFRACTION6(chain 'Q' and resid 1 through 10)

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