[English] 日本語
Yorodumi
- PDB-6dbf: Crystal Structure of VHH R303 in complex with InlB-LRR -

+
Open data


ID or keywords:

Loading...

-
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 / cell envelope / 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 / Leucine-rich repeat, SDS22-like subfamily / Alpha-Beta Horseshoe / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more