[English] 日本語
Yorodumi
- PDB-6p22: Photorhabdus Virulence Cassette (PVC) PAAR repeat protein Pvc10 i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6p22
TitlePhotorhabdus Virulence Cassette (PVC) PAAR repeat protein Pvc10 in complex with a T4 gp5 beta-helix fragment modified to mimic Pvc8, the central spike protein of PVC
Components
  • CHIMERA OF CENTRAL SPIKE PROTEINS GP5 FROM PHAGE T4 AND PVC8 FROM PVC
  • PAAR-REPEAT CENTRAL SPIKE TIP PROTEIN
KeywordsVIRAL PROTEIN / PVC / Photorhabdus laumondii / membrane piercing / central spike / cell puncturing device / PAAR-repeat motif / beta helix / T4 gp5 / contractile injection system / Pvc8 / Pvc10 / hydrolase
Function / homology
Function and homology information


symbiont entry into host cell via disruption of host cell wall peptidoglycan / virus tail, baseplate / viral tail assembly / symbiont entry into host cell via disruption of host cell envelope / virus tail / symbiont entry into host / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity ...symbiont entry into host cell via disruption of host cell wall peptidoglycan / virus tail, baseplate / viral tail assembly / symbiont entry into host cell via disruption of host cell envelope / virus tail / symbiont entry into host / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium / symbiont entry into host cell / identical protein binding
Similarity search - Function
Contractile injection system spike tip protein / Protein Gp5, N-terminal OB-fold domain / Gp5, C-terminal / Pre-baseplate central spike protein Gp5 / Gp5 N-terminal OB domain / Gp5 C-terminal repeat (3 copies) / Gp5/Type VI secretion system Vgr protein, OB-fold domain / Type VI secretion system/phage-baseplate injector OB domain / Vgr protein, OB-fold domain superfamily / T4-type lysozyme ...Contractile injection system spike tip protein / Protein Gp5, N-terminal OB-fold domain / Gp5, C-terminal / Pre-baseplate central spike protein Gp5 / Gp5 N-terminal OB domain / Gp5 C-terminal repeat (3 copies) / Gp5/Type VI secretion system Vgr protein, OB-fold domain / Type VI secretion system/phage-baseplate injector OB domain / Vgr protein, OB-fold domain superfamily / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme-like domain superfamily
Similarity search - Domain/homology
9-OCTADECENOIC ACID / PALMITIC ACID / STEARIC ACID / Pre-baseplate central spike protein Gp5 / Phage_base_V domain-containing protein / Uncharacterized protein
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Photorhabdus luminescens subsp. laumondii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.291 Å
AuthorsButh, S.A. / Shneider, M.M. / Leiman, P.G.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_144243 Switzerland
Citation
Journal: To Be Published
Title: Photorhabdus Virulence Cassette (PVC) PAAR repeat protein Pvc10 in complex with a T4 gp5 beta-helix fragment modified to mimic Pvc8, the central spike protein of PVC
Authors: Buth, S.A. / Shneider, M.M. / Leiman, P.G.
#1: Journal: Nature / Year: 2013
Title: PAAR-repeat proteins sharpen and diversify the type VI secretion system spike.
Authors: Shneider, M.M. / Buth, S.A. / Ho, B.T. / Basler, M. / Mekalanos, J.J. / Leiman, P.G.
#2: Journal: Viruses / Year: 2015
Title: Structure and Biophysical Properties of a Triple-Stranded Beta-Helix Comprising the Central Spike of Bacteriophage T4.
Authors: Buth, S.A. / Menin, L. / Shneider, M.M. / Engel, J. / Boudko, S.P. / Leiman, P.G.
History
DepositionMay 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CHIMERA OF CENTRAL SPIKE PROTEINS GP5 FROM PHAGE T4 AND PVC8 FROM PVC
B: CHIMERA OF CENTRAL SPIKE PROTEINS GP5 FROM PHAGE T4 AND PVC8 FROM PVC
C: CHIMERA OF CENTRAL SPIKE PROTEINS GP5 FROM PHAGE T4 AND PVC8 FROM PVC
D: PAAR-REPEAT CENTRAL SPIKE TIP PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5538
Polymers44,7064
Non-polymers8484
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25840 Å2
ΔGint-77 kcal/mol
Surface area16490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.305, 56.963, 222.994
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 4 molecules ABCD

#1: Protein CHIMERA OF CENTRAL SPIKE PROTEINS GP5 FROM PHAGE T4 AND PVC8 FROM PVC / T4 CELL-PUNCTURING DEVICE PROTEIN GP5 / PVC CENTRAL SPIKE PROTEIN PVC8


Mass: 10011.937 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01) (bacteria)
Plasmid: PEEVA2 / Strain: DSM 15139 / CIP 105565 / TT01 / Gene: plu1723 / Details (production host): a PET-23A DERIVATIVE / Production host: Escherichia coli (E. coli) / Variant (production host): B834 / References: UniProt: P16009, UniProt: Q7N647, lysozyme
#2: Protein PAAR-REPEAT CENTRAL SPIKE TIP PROTEIN


Mass: 14669.818 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01) (bacteria)
Strain: DSM 15139 / CIP 105565 / TT01 / Gene: plu1721 / Variant: TT01 / Plasmid: pATE / Details (production host): A PACYCDUET-1 DERIVATIVE / Production host: Escherichia coli (E. coli) / Variant (production host): B834 / References: UniProt: Q7N648

-
Non-polymers , 5 types, 145 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-STE / STEARIC ACID


Mass: 284.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36O2
#5: Chemical ChemComp-ELA / 9-OCTADECENOIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#6: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsT4 gp5 beta helix fragment with a modified C-terminus to mimic the PluTT01m_08915 PVC central spike ...T4 gp5 beta helix fragment with a modified C-terminus to mimic the PluTT01m_08915 PVC central spike protein Pvc8. Chimera consists of a T4 gp5 fragment G484-Y565 extended by the D523-Q533 C-terminal fragment of Pvc8 protein.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: MPD 28-34% PEG 2000 8-18% 100 mM Imidazole pH 8.0 / PH range: 8

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 26, 2013 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 37669 / % possible obs: 99.2 % / Redundancy: 6.2 % / Biso Wilson estimate: 45.19 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.125 / Net I/σ(I): 9.78
Reflection shellResolution: 2.29→2.43 Å / Mean I/σ(I) obs: 2.05 / Num. unique obs: 5838 / CC1/2: 0.95 / Rrim(I) all: 0.702 / % possible all: 96

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSMarch 30, 2013data reduction
X-GENMarch 30, 2013data scaling
PHASER2.5.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JJ2

4jj2


Resolution: 2.291→45.213 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 25.36
RfactorNum. reflection% reflection
Rfree0.2224 1891 5.05 %
Rwork0.1819 --
obs0.184 37478 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 49.2 Å2
Refinement stepCycle: LAST / Resolution: 2.291→45.213 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3084 0 59 141 3284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023186
X-RAY DIFFRACTIONf_angle_d0.4834311
X-RAY DIFFRACTIONf_dihedral_angle_d11.1861898
X-RAY DIFFRACTIONf_chiral_restr0.051508
X-RAY DIFFRACTIONf_plane_restr0.003559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2907-2.34790.32861200.28122238X-RAY DIFFRACTION90
2.3479-2.41140.34921360.26452552X-RAY DIFFRACTION99
2.4114-2.48240.25351350.26212607X-RAY DIFFRACTION99
2.4824-2.56250.27461400.24812553X-RAY DIFFRACTION100
2.5625-2.65410.2591360.23032574X-RAY DIFFRACTION100
2.6541-2.76030.32251370.2272517X-RAY DIFFRACTION100
2.7603-2.88590.28371390.21872616X-RAY DIFFRACTION100
2.8859-3.0380.2491360.20342537X-RAY DIFFRACTION100
3.038-3.22830.23961340.18952560X-RAY DIFFRACTION100
3.2283-3.47750.22111420.16282599X-RAY DIFFRACTION100
3.4775-3.82730.20821360.1412556X-RAY DIFFRACTION99
3.8273-4.38070.18391350.14392578X-RAY DIFFRACTION100
4.3807-5.51770.13911340.13542532X-RAY DIFFRACTION99
5.5177-45.22210.22571310.19072568X-RAY DIFFRACTION100
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)
11.24960.0374-0.24870.152-0.19040.2670.35370.5836-0.5301-0.4257-0.3088-0.22140.4071-0.2247-0.00750.7132-0.0648-0.04320.67060.09560.43136.213267.958218.6718
20.1361-0.01350.13530.0020.02060.2825-0.14910.69510.2873-0.28010.0427-0.0070.01020.1845-0.00080.4639-0.1102-0.07740.42690.05620.4847-1.050563.520930.1664
30.61660.4451-0.09940.66860.54971.1172-0.19030.2350.0129-0.27640.11330.33060.1371-0.0688-0.00050.297-0.0099-0.03890.29640.03870.40194.282165.968242.5752
40.46660.25690.35790.63810.2950.2951-0.1380.05620.3789-0.21140.17220.3877-0.0544-0.14560.00010.2201-0.01330.02620.2607-0.00710.3335.231268.07355.429
50.2732-0.23580.06950.2923-0.04880.1573-0.1309-0.18660.10530.07360.07990.1490.075-0.060700.3734-0.0199-0.0130.3061-0.02310.365515.574467.904262.5276
60.207-0.17320.19340.141-0.16110.2010.27120.28040.1207-0.671-0.10220.16510.54130.30790.00040.5181-0.0783-0.04110.51710.03870.46637.038762.706672.7665
73.336-0.0197-0.5240.5410.65590.85940.01620.80120.3542-0.29570.12350.0222-0.077-0.23390.1740.5161-0.1869-0.06150.59290.05140.31451.335665.557224.1815
80.16860.0838-0.2790.2664-0.30790.5863-0.40360.3412-0.0543-0.12770.21360.21140.27610.0576-0.02370.4503-0.0799-0.03080.43440.00250.5019-0.53660.540335.6133
90.20320.25140.24540.43110.2110.3444-0.15770.1520.1739-0.11710.09910.1923-0.0833-0.0380.00010.327-0.0184-0.03310.43320.05280.44143.218669.15345.0304
100.4715-0.1888-0.4040.3958-0.18650.697-0.0032-0.16270.02780.0315-0.10840.23110.03870.0081-0.00010.22160.0084-0.02660.2351-0.02110.324811.602367.003553.3428
110.2905-0.3264-0.21420.43540.41950.55650.40280.1691-0.2644-0.0909-0.20460.19730.0305-0.1451-00.32390.0281-0.0480.3560.02930.373110.431960.61464.1728
120.10310.02760.12560.21720.09350.20750.10980.26910.3755-0.0422-0.11360.3965-0.4155-0.06420.00090.46720.0158-0.00280.3107-0.03810.390413.765572.964770.6334
131.1683-0.6476-1.96640.7041.15813.3233-0.22360.2812-0.15990.2672-0.0594-0.17590.5139-0.6557-0.28210.4009-0.198-0.16870.6750.05670.5431-5.052676.254521.8569
140.4217-0.2574-0.20210.427-0.20420.4628-0.1470.19120.1509-0.73430.19710.1636-0.04410.0007-0.01250.5227-0.0608-0.08020.4664-0.01720.38070.445562.163626.9656
150.2274-0.16050.01620.38130.38770.5867-0.18730.4219-0.0282-0.46950.2833-0.24230.2717-0.4360.00020.4527-0.0396-0.0540.50690.04510.5336-3.118269.50637.7142
160.8764-0.40320.25120.49370.28580.5603-0.18520.0643-0.0673-0.21760.20820.34420.0023-0.1515-0.00030.3772-0.0462-0.00630.35880.00310.36168.358466.71444.0538
170.54320.2731-0.1980.41940.28220.5982-0.278-0.5079-0.30330.17460.1710.10040.03490.0452-0.00240.30780.01820.00620.312-0.02110.42438.337561.413554.9301
180.2983-0.0986-0.1970.1454-0.18250.64980.06770.11980.25280.40270.0459-0.1322-0.0771-0.0282-0.00060.36030.0065-0.00130.3901-0.0170.371311.621866.019766.7684
190.0062-0.03930.00880.2272-0.01310.0505-0.26170.15670.4422-0.15580.14950.663-0.3948-0.4890.00040.50640.0402-0.02730.4997-0.02430.324512.851867.323187.0178
200.9725-0.02480.57790.76550.79851.190.0399-0.186-0.01970.21510.02120.0527-0.2623-0.5138-0.00010.5344-0.0179-0.01670.4219-0.03480.349619.192268.911792.212
210.0784-0.02760.0690.0293-0.02580.0605-0.0974-0.5008-0.0239-0.26870.3391-0.8250.30290.3369-0.00040.5787-0.03690.0140.5258-0.01330.443626.353366.441789.8684
220.5864-0.17060.61690.0468-0.17620.64110.0981-0.32150.10340.306-0.00650.12460.2886-0.25320.00010.6237-0.0501-0.05580.4550.01610.294622.739664.057999.3978
230.34910.0065-0.05930.08670.22780.59270.0243-0.24310.03050.0282-0.1751-0.07310.130.1845-0.00010.4336-0.031-0.06750.49950.02650.330421.876662.353691.791
240.00150.03010.10660.09950.29211.06580.1608-0.4629-0.13680.21140.13840.07580.2057-0.62780.01670.6082-0.0015-0.02260.5288-0.04450.331220.461263.9841101.3959
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 483 through 491 )
2X-RAY DIFFRACTION2chain 'A' and (resid 492 through 511 )
3X-RAY DIFFRACTION3chain 'A' and (resid 512 through 536 )
4X-RAY DIFFRACTION4chain 'A' and (resid 537 through 553 )
5X-RAY DIFFRACTION5chain 'A' and (resid 554 through 567 )
6X-RAY DIFFRACTION6chain 'A' and (resid 568 through 576 )
7X-RAY DIFFRACTION7chain 'B' and (resid 484 through 503 )
8X-RAY DIFFRACTION8chain 'B' and (resid 504 through 518 )
9X-RAY DIFFRACTION9chain 'B' and (resid 519 through 536 )
10X-RAY DIFFRACTION10chain 'B' and (resid 537 through 553 )
11X-RAY DIFFRACTION11chain 'B' and (resid 554 through 567 )
12X-RAY DIFFRACTION12chain 'B' and (resid 568 through 576 )
13X-RAY DIFFRACTION13chain 'C' and (resid 483 through 488 )
14X-RAY DIFFRACTION14chain 'C' and (resid 489 through 506 )
15X-RAY DIFFRACTION15chain 'C' and (resid 507 through 519 )
16X-RAY DIFFRACTION16chain 'C' and (resid 520 through 537 )
17X-RAY DIFFRACTION17chain 'C' and (resid 538 through 553 )
18X-RAY DIFFRACTION18chain 'C' and (resid 554 through 576 )
19X-RAY DIFFRACTION19chain 'D' and (resid 2 through 13 )
20X-RAY DIFFRACTION20chain 'D' and (resid 14 through 49 )
21X-RAY DIFFRACTION21chain 'D' and (resid 50 through 53 )
22X-RAY DIFFRACTION22chain 'D' and (resid 54 through 86 )
23X-RAY DIFFRACTION23chain 'D' and (resid 87 through 107 )
24X-RAY DIFFRACTION24chain 'D' and (resid 108 through 138 )

+
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://pdbjlvh1.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