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- PDB-7kjk: The Neck region of Phage XM1 (6-fold symmetry) -

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Basic information

Entry
Database: PDB / ID: 7kjk
TitleThe Neck region of Phage XM1 (6-fold symmetry)
Components
  • Collar spike protein
  • Head completion protein
  • Tail sheath protein
  • Tail terminator protein
  • Tail tube protein
KeywordsVIRAL PROTEIN / Myoviridae / Phage / 6-fold neck region
Biological speciesVibrio phage XM1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsWang, Z. / Klose, T. / Jiang, W. / Kuhn, R.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: Biorxiv / Year: 2021
Title: Structure of Vibrio phage XM1, a simple contractile DNA injection machine
Authors: Wang, Z. / Fokine, A. / Guo, X. / Jiang, W. / Rossmann, M.G. / Kuhn, R.J. / Luo, Z.H. / Klose, T.
History
DepositionOct 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Assembly

Deposited unit
A5: Tail terminator protein
B5: Tail terminator protein
C5: Tail terminator protein
D5: Tail terminator protein
E5: Tail terminator protein
F5: Tail terminator protein
A3: Collar spike protein
B3: Collar spike protein
C3: Collar spike protein
D3: Collar spike protein
E3: Collar spike protein
F3: Collar spike protein
G3: Collar spike protein
H3: Collar spike protein
I3: Collar spike protein
J3: Collar spike protein
K3: Collar spike protein
L3: Collar spike protein
M3: Collar spike protein
N3: Collar spike protein
O3: Collar spike protein
P3: Collar spike protein
Q3: Collar spike protein
R3: Collar spike protein
A4: Head completion protein
B4: Head completion protein
C4: Head completion protein
D4: Head completion protein
E4: Head completion protein
F4: Head completion protein
A7: Tail tube protein
B7: Tail tube protein
C7: Tail tube protein
D7: Tail tube protein
E7: Tail tube protein
F7: Tail tube protein
A6: Tail sheath protein
B6: Tail sheath protein
C6: Tail sheath protein
D6: Tail sheath protein
E6: Tail sheath protein
F6: Tail sheath protein


Theoretical massNumber of molelcules
Total (without water)2,232,19042
Polymers2,232,19042
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "F4"
d_2ens_1chain "B4"
d_3ens_1chain "C4"
d_4ens_1chain "D4"
d_5ens_1chain "E4"
d_6ens_1chain "A4"
d_1ens_2chain "A5"
d_2ens_2chain "B5"
d_3ens_2chain "C5"
d_4ens_2chain "D5"
d_5ens_2chain "E5"
d_6ens_2chain "F5"
d_1ens_3chain "B6"
d_2ens_3chain "A6"
d_3ens_3chain "C6"
d_4ens_3chain "D6"
d_5ens_3chain "E6"
d_6ens_3chain "F6"
d_1ens_4chain "F7"
d_2ens_4chain "E7"
d_3ens_4chain "C7"
d_4ens_4chain "D7"
d_5ens_4chain "A7"
d_6ens_4chain "B7"

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4

NCS oper:
IDCodeMatrixVector
1given(-0.490844053886, 0.871243703639, -0.00255414034106), (-0.871245781934, -0.49084673861, -0.000516389096312), (-0.00170359220515, 0.0019718174812, 0.999996604849)61.7915639853, 242.766366017, 0.00201461411609
2given(0.496681569481, -0.867931917847, 0.00126669631454), (0.86792264225, 0.496682279013, 0.00412320075258), (-0.00420780314918, -0.000948523408839, 0.999990697305)140.439089128, -36.7336173292, 0.525678392784
3given(-0.5105531431, -0.859845274424, 0.00126179289687), (0.859845737734, -0.510550796692, 0.00178642043418), (-0.000891835799706, 0.00199700981185, 0.999997608287)242.194449067, 68.2036053224, -0.0351876015207
4given(-0.999900477286, 0.0133633474576, -0.00452288259494), (-0.0133697000287, -0.999909673099, 0.00137723053621), (-0.00450406964679, 0.00143756305405, 0.999988823322)202.574707564, 207.710990018, 0.412142936645
5given(0.501075922732, 0.865399995459, 0.00240156551885), (-0.865403129714, 0.501072001334, 0.00206701752224), (0.000585439713491, -0.00311405502849, 0.999994979948)-39.0165727542, 139.16736124, 0.162751883104
6given(0.507670673812, -0.861435125902, 0.0141425179303), (0.86131258839, 0.507847999821, 0.0151998078352), (-0.0202758978195, 0.00446463203945, 0.999784454284)138.031288021, -38.0660611101, 1.04830159028
7given(-0.493183386165, -0.869923671646, -0.00171846455039), (0.869883232355, -0.493177978317, 0.00886813232332), (-0.00856210710412, 0.0028787520304, 0.999959200722)241.808750051, 65.1965810208, 0.326073759596
8given(-0.999702394758, -0.0143509804669, -0.0197274244244), (0.01428897059, -0.999892525351, 0.00328071123234), (-0.0197723856492, 0.00299785028806, 0.999800012832)206.333708599, 205.201319057, 1.23135510118
9given(-0.499227909075, 0.866469213459, -0.00161149861813), (-0.866421455616, -0.499218496768, -0.00973415286271), (-0.00923883369233, -0.00346332380183, 0.999951323485)62.7260513998, 243.624994902, 1.26464913545
10given(0.502694605143, 0.864464033664, 0.00026164980275), (-0.864462149214, 0.502694101855, -0.00195768676485), (-0.00182387960999, 0.000757932224425, 0.999998049499)-38.7636271837, 139.312030733, 0.0812601821528
11given(0.50056145032, 0.865700919613, 0.000390172768066), (-0.865700723667, 0.500560870351, 0.00103543014519), (0.000701067608516, -0.000856069262851, 0.999999387825)-38.6837450578, 139.435670886, -0.010899113731
12given(0.500831088366, -0.865543969356, -0.00136309855666), (0.865544801691, 0.500831503064, 4.24911530166E-5), (0.000645904737711, -0.00120110376032, 0.999999070078)140.270975261, -35.7221520674, 0.0164747411302
13given(-0.497434884348, -0.867499601624, -0.0017254030792), (0.867500964811, -0.497435491665, -8.76600544109E-5), (-0.000782231666743, -0.00154039400492, 0.999998507649)241.767664272, 66.7712865265, 0.307645823504
14given(-0.999983184931, -0.00116469769872, -0.0056809624213), (0.00116436756121, -0.999999320238, 6.14200002022E-5), (-0.00568103009533, 5.48042390608E-5, 0.999983861317)203.36575166, 206.643027678, 0.200041148281
15given(-0.499596088423, 0.866258129916, 0.000775104672417), (-0.866256983308, -0.499596688612, 0.00140982213336), (0.00160850961243, 3.29017879247E-5, 0.999998705806)62.6478434253, 242.797557159, -0.17136863343
16given(-0.999994012375, 0.00315262996115, 0.0014269332636), (-0.00315460310492, -0.999994068356, -0.00138265433903), (0.00142256580204, -0.00138714746832, 0.999998026062)202.652968715, 207.090731394, -0.0196308965193
17given(-0.501053510038, 0.865415222046, -0.00136876952153), (-0.865411664991, -0.501055376146, -0.00248196133795), (-0.00283375644986, -5.9046329544E-5, 0.999995983161)63.0283657717, 243.134510531, 0.310324435508
18given(0.496700885345, 0.867919337993, -0.00206233720597), (-0.867920718525, 0.496702601592, 0.00038977716502), (0.00136266339459, 0.00159634252669, 0.999997797417)-38.5114679102, 140.19096316, -0.395140806667
19given(0.495598602258, -0.868551031656, -0.00106341394368), (0.868550795451, 0.495595974568, 0.00203610228933), (-0.00124143507417, -0.00193271847532, 0.999997361716)141.072468596, -36.1564594805, 0.371643208526
20given(-0.503701700783, -0.863877550612, 0.000417345627797), (0.863876839791, -0.503700506529, 0.00161412389571), (-0.00118418819329, 0.00117357217359, 0.999998610212)242.013020147, 67.681878034, 0.0389523102876

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Components

#1: Protein
Tail terminator protein


Mass: 18236.037 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Vibrio phage XM1 (virus)
#2: Protein
Collar spike protein


Mass: 90692.562 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Vibrio phage XM1 (virus)
#3: Protein
Head completion protein


Mass: 13045.932 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Vibrio phage XM1 (virus)
#4: Protein
Tail tube protein


Mass: 15665.332 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Vibrio phage XM1 (virus)
#5: Protein
Tail sheath protein


Mass: 53006.762 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Vibrio phage XM1 (virus)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Vibrio phage XM1 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Vibrio phage XM1 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Vibrio rotiferianus
Virus shellDiameter: 640 nm / Triangulation number (T number): 7
Buffer solutionpH: 7.5 / Details: 50 mM Tris, pH 7.5, 100 mM NaCl, 8 mM MgSO4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: PELCO Ultrathin Carbon with Lacey Carbon
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 30 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: DIRECT ELECTRON DE-16 (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
EM software
IDNameCategory
1EMAN2particle selection
4CTFFINDCTF correction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 10615
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10615 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 117.92 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.008959988
ELECTRON MICROSCOPYf_angle_d0.914881510
ELECTRON MICROSCOPYf_chiral_restr0.05329684
ELECTRON MICROSCOPYf_plane_restr0.005410548
ELECTRON MICROSCOPYf_dihedral_angle_d15.05428280
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2B4ELECTRON MICROSCOPYNCS constraints0.000715618407636
ens_1d_3C4ELECTRON MICROSCOPYNCS constraints0.00071554647701
ens_1d_4D4ELECTRON MICROSCOPYNCS constraints0.00071253546804
ens_1d_5E4ELECTRON MICROSCOPYNCS constraints0.000701833271055
ens_1d_6A4ELECTRON MICROSCOPYNCS constraints0.000705826780497
ens_2d_2B5ELECTRON MICROSCOPYNCS constraints0.125989642891
ens_2d_3C5ELECTRON MICROSCOPYNCS constraints0.125977593673
ens_2d_4D5ELECTRON MICROSCOPYNCS constraints0.125989826261
ens_2d_5E5ELECTRON MICROSCOPYNCS constraints0.125974849135
ens_2d_6F5ELECTRON MICROSCOPYNCS constraints0.089465960932
ens_3d_2A6ELECTRON MICROSCOPYNCS constraints0.0520770807838
ens_3d_3C6ELECTRON MICROSCOPYNCS constraints0.0734960220917
ens_3d_4D6ELECTRON MICROSCOPYNCS constraints0.000695801503048
ens_3d_5E6ELECTRON MICROSCOPYNCS constraints0.0520816628813
ens_3d_6F6ELECTRON MICROSCOPYNCS constraints0.000702316365209
ens_4d_2E7ELECTRON MICROSCOPYNCS constraints0.000691833102394
ens_4d_3C7ELECTRON MICROSCOPYNCS constraints0.000693912904321
ens_4d_4D7ELECTRON MICROSCOPYNCS constraints0.000696941421207
ens_4d_5A7ELECTRON MICROSCOPYNCS constraints0.000711415683836
ens_4d_6B7ELECTRON MICROSCOPYNCS constraints0.000701083798755

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