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- PDB-6dbf: Crystal Structure of VHH R303 in complex with InlB-LRR -

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Basic information

Entry
Database: PDB / ID: 6dbf
TitleCrystal Structure of VHH R303 in complex with InlB-LRR
Components
  • InlB specific VHH R303
  • Listeria virulence factor InlB
KeywordsIMMUNE SYSTEM / nanobody VHH Listeria Internalin
Function / homology
Function and homology information


entry of bacterium into host cell / peptidoglycan-based cell wall / InlB-mediated entry of Listeria monocytogenes into host cell / heparin binding / lipid binding / cell surface / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
GW domain / GW domain superfamily / GW (Gly-Tryp) dipeptide domain / GW domain profile. / Listeria/Bacterioides repeat / Listeria-Bacteroides repeat domain superfamily / Listeria-Bacteroides repeat domain (List_Bact_rpt) / Leucine-rich repeat-containing adjacent domain / LRR adjacent / Internalin, N-terminal ...GW domain / GW domain superfamily / GW (Gly-Tryp) dipeptide domain / GW domain profile. / Listeria/Bacterioides repeat / Listeria-Bacteroides repeat domain superfamily / Listeria-Bacteroides repeat domain (List_Bact_rpt) / Leucine-rich repeat-containing adjacent domain / LRR adjacent / Internalin, N-terminal / Bacterial adhesion/invasion protein N terminal / : / Copper resistance protein CopC/internalin, immunoglobulin-like / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat, SDS22-like subfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Immunoglobulin E-set / Alpha Beta
Similarity search - Domain/homology
Internalin B / Internalin B
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
Camelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsBrooks, C.L. / Toride King, M. / Huh, I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)SC3GM112532 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural basis of VHH-mediated neutralization of the food-borne pathogenListeria monocytogenes.
Authors: King, M.T. / Huh, I. / Shenai, A. / Brooks, T.M. / Brooks, C.L.
History
DepositionMay 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 12, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / citation_author / entity_src_gen
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Listeria virulence factor InlB
B: InlB specific VHH R303


Theoretical massNumber of molelcules
Total (without water)41,4652
Polymers41,4652
Non-polymers00
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-4 kcal/mol
Surface area14650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.964, 82.964, 64.216
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Listeria virulence factor InlB


Mass: 25678.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Plasmid: pET15-TEV / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q45GD4, UniProt: P0DQD3*PLUS
#2: Antibody InlB specific VHH R303


Mass: 15786.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Plasmid: pJSJF2H / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O
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: 2.66 Å3/Da / Density % sol: 53.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris, 25% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 12, 2012
Details: Vertical Focusing Mirror: ultra-low expansion (ULE) titanium siliicate flat mirror with Pt, Uncoated, and Pd strips
RadiationMonochromator: ACCEL/BRUKER double crystal monochromator (DCM), featuring indirectly cryo-cooled first crystal and sagittally focusing second crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.55→58.664 Å / Num. obs: 62224 / % possible obs: 98.3 % / Redundancy: 7.6 % / Biso Wilson estimate: 17.74 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 17.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.55-1.597.40.4334.3196.9
6.93-58.6670.03434.4194.2

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DBA, 1OTM

6dba

1otm


Resolution: 1.55→58.664 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.89
RfactorNum. reflection% reflection
Rfree0.1626 3156 5.08 %
Rwork0.1375 --
obs0.1387 62183 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.37 Å2 / Biso mean: 26.3228 Å2 / Biso min: 10.44 Å2
Refinement stepCycle: final / Resolution: 1.55→58.664 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2523 0 0 382 2905
Biso mean---39.38 -
Num. residues----329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172659
X-RAY DIFFRACTIONf_angle_d1.3743641
X-RAY DIFFRACTIONf_chiral_restr0.078439
X-RAY DIFFRACTIONf_plane_restr0.009466
X-RAY DIFFRACTIONf_dihedral_angle_d11.7861631
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.57320.18331300.18192527265796
1.5732-1.59770.2431320.16912516264897
1.5977-1.62390.20681330.16752518265197
1.6239-1.65190.18211370.16462555269297
1.6519-1.6820.16711660.15692456262297
1.682-1.71430.19131260.15092550267697
1.7143-1.74930.19521310.14472579271098
1.7493-1.78740.17031290.15312511264097
1.7874-1.8290.17441320.14552541267398
1.829-1.87470.17411520.14242566271898
1.8747-1.92540.19081490.13812523267298
1.9254-1.9820.15491300.1342596272699
1.982-2.0460.13751350.12652554268998
2.046-2.11910.15371240.12562563268799
2.1191-2.2040.14831360.12722588272498
2.204-2.30430.13971320.12792595272799
2.3043-2.42580.15351180.12442598271699
2.4258-2.57780.15191430.12722593273699
2.5778-2.77680.16071530.13825762729100
2.7768-3.05620.16471470.13442610275799
3.0562-3.49840.15261530.128626132766100
3.4984-4.40750.13541250.122526472772100
4.4075-58.70650.19431430.16312652279598
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)
11.61850.8575-0.43181.9397-1.38351.86160.0179-0.0944-0.14160.12120.07430.13380.1174-0.1248-0.08320.2088-0.0070.01080.14210.01290.1678-3.908340.90135.8141
22.7854-0.97870.85533.0551-0.63232.62420.0048-0.10560.00880.04380.07990.30790.1138-0.2384-0.06950.1345-0.0270.02330.14430.02880.1768-3.031456.933629.0433
31.4495-0.1974-0.29131.5091-0.27631.3249-0.007-0.03850.07020.01690.03620.0267-0.0051-0.0054-0.02720.1166-0.0020.01270.11360.00210.13241.613768.737725.2815
41.73180.18690.65342.99040.9484.0130.0784-0.0620.0727-0.1276-0.0189-0.0134-0.0218-0.1789-0.03730.1197-0.01520.03880.17990.03510.16469.296573.999719.3992
54.5548-0.23322.46760.699-0.21862.87150.50230.7322-0.2041-0.0942-0.2471-0.15620.65290.7248-0.19420.25440.0949-0.0190.3619-0.09420.278632.651846.952323.9449
62.0276-0.6081.9851.6034-1.02962.0791-0.04680.48570.02760.01260.0322-0.23690.08070.54650.04340.19460.05490.01390.4115-0.01930.220430.305851.756120.7299
73.2011-1.1131.14342.3787-0.69843.21520.2110.2638-0.1396-0.282-0.08310.07830.27210.095-0.18370.15480.0029-0.01610.1568-0.02240.144519.989253.993822.2345
84.0398-0.22790.01414.1641-1.27184.5658-0.0353-0.10940.12830.17960.13820.16080.1122-0.1688-0.11950.1326-0.0032-0.00410.141-0.00890.146222.232855.850130.2758
92.54211.2141-3.77893.93280.17347.73760.1194-1.01441.19940.59440.0674-0.1745-0.99940.0907-0.19520.34050.0371-0.05330.2956-0.11160.28729.465756.640538.4256
103.0422-0.10891.62562.53480.07565.29010.08460.55320.3272-0.1074-0.0615-0.283-0.19020.4579-0.03610.12530.00670.03040.28270.03440.208429.849557.828222.4863
116.15393.8942-1.16328.8694-1.19684.87480.1681-0.7065-0.2140.214-0.0028-0.11710.30990.3772-0.19050.19420.0386-0.09090.26690.01130.256635.53748.201837.1344
123.0915-0.70291.00471.33340.16841.44350.1260.1563-0.07570.0147-0.072-0.10070.0450.1042-0.04930.13320.0044-0.00010.1302-0.00540.150217.955952.106926.8123
137.3571-0.60.19842.8993-2.1313.38310.17320.4749-0.44930.1406-0.0071-0.09410.31930.2351-0.13430.1580.0157-0.0320.1567-0.06740.188117.056546.072923.9795
147.1522-1.13784.13762.7664-1.63244.82420.1671-0.0534-0.47080.3671-0.0733-0.25760.27940.1908-0.04180.31090.1449-0.20820.3107-0.11450.471635.738941.782832.0083
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 37 through 124 )A37 - 124
2X-RAY DIFFRACTION2chain 'A' and (resid 125 through 158 )A125 - 158
3X-RAY DIFFRACTION3chain 'A' and (resid 159 through 224 )A159 - 224
4X-RAY DIFFRACTION4chain 'A' and (resid 225 through 244 )A225 - 244
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 17 )B1 - 17
6X-RAY DIFFRACTION6chain 'B' and (resid 18 through 25 )B18 - 25
7X-RAY DIFFRACTION7chain 'B' and (resid 26 through 39 )B26 - 39
8X-RAY DIFFRACTION8chain 'B' and (resid 40 through 60 )B40 - 60
9X-RAY DIFFRACTION9chain 'B' and (resid 61 through 67 )B61 - 67
10X-RAY DIFFRACTION10chain 'B' and (resid 68 through 83 )B68 - 83
11X-RAY DIFFRACTION11chain 'B' and (resid 84 through 91 )B84 - 91
12X-RAY DIFFRACTION12chain 'B' and (resid 92 through 107 )B92 - 107
13X-RAY DIFFRACTION13chain 'B' and (resid 108 through 116 )B108 - 116
14X-RAY DIFFRACTION14chain 'B' and (resid 117 through 123 )B117 - 123

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