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- PDB-7kh1: Baseplate Complex for Myoviridae Phage XM1 -

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Basic information

Entry
Database: PDB / ID: 7kh1
TitleBaseplate Complex for Myoviridae Phage XM1
Components
  • (baseplate wedge protein, ...) x 2
  • baseplate organization protein, gp11
  • baseplate stabilizing protein, gp12
  • tail sheath initiator protein, gp15
  • tail sheath protein, gp6
  • tail tube protein, gp7
KeywordsVIRUS / Myoviridae / Phage / Baseplate complex
Biological speciesVibrio phage XM1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 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 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 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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Structure visualization

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  • Simplified surface model + fitted atomic model
  • EMDB-22873
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Structure viewerMolecule:
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Assembly

Deposited unit
A1: tail tube protein, gp7
B1: tail tube protein, gp7
C1: tail tube protein, gp7
D1: tail tube protein, gp7
E1: tail tube protein, gp7
F1: tail tube protein, gp7
A2: baseplate wedge protein, gp17
B2: baseplate wedge protein, gp17
C2: baseplate wedge protein, gp17
D2: baseplate wedge protein, gp17
E2: baseplate wedge protein, gp17
F2: baseplate wedge protein, gp17
A3: baseplate organization protein, gp11
B3: baseplate organization protein, gp11
C3: baseplate organization protein, gp11
D3: baseplate organization protein, gp11
E3: baseplate organization protein, gp11
F3: baseplate organization protein, gp11
A4: baseplate stabilizing protein, gp12
B4: baseplate stabilizing protein, gp12
C4: baseplate stabilizing protein, gp12
D4: baseplate stabilizing protein, gp12
E4: baseplate stabilizing protein, gp12
F4: baseplate stabilizing protein, gp12
A5: baseplate wedge protein, gp16
B5: baseplate wedge protein, gp16
C5: baseplate wedge protein, gp16
D5: baseplate wedge protein, gp16
E5: baseplate wedge protein, gp16
F5: baseplate wedge protein, gp16
G5: baseplate wedge protein, gp16
H5: baseplate wedge protein, gp16
I5: baseplate wedge protein, gp16
J5: baseplate wedge protein, gp16
K5: baseplate wedge protein, gp16
L5: baseplate wedge protein, gp16
A6: tail sheath protein, gp6
B6: tail sheath protein, gp6
C6: tail sheath protein, gp6
D6: tail sheath protein, gp6
E6: tail sheath protein, gp6
F6: tail sheath protein, gp6
A7: tail sheath initiator protein, gp15
B7: tail sheath initiator protein, gp15
C7: tail sheath initiator protein, gp15
D7: tail sheath initiator protein, gp15
E7: tail sheath initiator protein, gp15
F7: tail sheath initiator protein, gp15


Theoretical massNumber of molelcules
Total (without water)1,434,34648
Polymers1,434,34648
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "E1"
d_2ens_1chain "B1"
d_3ens_1chain "C1"
d_4ens_1chain "D1"
d_5ens_1chain "A1"
d_6ens_1chain "F1"
d_1ens_2chain "B2"
d_2ens_2chain "A2"
d_3ens_2chain "E2"
d_4ens_2chain "D2"
d_5ens_2chain "F2"
d_6ens_2chain "C2"
d_1ens_3chain "E3"
d_2ens_3chain "B3"
d_3ens_3chain "C3"
d_4ens_3chain "D3"
d_5ens_3chain "A3"
d_6ens_3chain "F3"
d_1ens_4chain "B4"
d_2ens_4chain "A4"
d_3ens_4chain "C4"
d_4ens_4chain "D4"
d_5ens_4chain "F4"
d_6ens_4chain "E4"
d_1ens_5chain "A6"
d_2ens_5chain "B6"
d_3ens_5chain "C6"
d_4ens_5chain "D6"
d_5ens_5chain "E6"
d_6ens_5chain "F6"
d_1ens_6chain "B7"
d_2ens_6chain "E7"
d_3ens_6chain "C7"
d_4ens_6chain "A7"
d_5ens_6chain "D7"
d_6ens_6chain "F7"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERPHEE1 - 142
d_21ens_1SERPHEB1 - 142
d_31ens_1SERPHEC1 - 142
d_41ens_1SERPHED1 - 142
d_51ens_1SERPHEA1 - 142
d_61ens_1SERPHEF1 - 142
d_11ens_2METILEH1 - 173
d_21ens_2METILEG1 - 173
d_31ens_2METILEK1 - 173
d_41ens_2METILEJ1 - 173
d_51ens_2METILEL1 - 173
d_61ens_2METILEI1 - 173
d_11ens_3METGLYQ1 - 250
d_21ens_3METGLYN1 - 250
d_31ens_3METGLYO1 - 250
d_41ens_3METGLYP1 - 250
d_51ens_3METGLYM1 - 250
d_61ens_3METGLYR1 - 250
d_11ens_4METGLNT1 - 118
d_21ens_4METGLNS1 - 118
d_31ens_4METGLNU1 - 118
d_41ens_4METGLNV1 - 118
d_51ens_4METGLNX1 - 118
d_61ens_4METGLNW1 - 118
d_11ens_5METLEUKA1 - 497
d_21ens_5METLEULA1 - 497
d_31ens_5METLEUMA1 - 497
d_41ens_5METLEUNA1 - 497
d_51ens_5METLEUOA1 - 497
d_61ens_5METLEUPA1 - 497
d_11ens_6METGLURA1 - 110
d_21ens_6METGLUUA1 - 110
d_31ens_6METGLUSA1 - 110
d_41ens_6METGLUQA1 - 110
d_51ens_6METGLUTA1 - 110
d_61ens_6METGLUVA1 - 110

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4
ens_5
ens_6

NCS oper:
IDCodeMatrixVector
1given(-0.999991185652, 0.00299090051978, 0.00294671568518), (-0.00298329989627, -0.999992220745, 0.0025803820883), (0.00295441042806, 0.00257156840731, 0.999992329218)211.886645538, 214.089187772, -0.518235950413
2given(-0.496902300921, 0.867806448336, -0.000267519289864), (-0.867806294417, -0.496902372306, -0.000517463077208), (-0.000581988764948, -2.49736700847E-5, 0.999999830333)66.0916561199, 252.256182654, 0.0338214492206
3given(0.504136230345, 0.863617162331, -0.00347248919283), (-0.863621272432, 0.504140847055, 0.000551483396246), (0.0022268941688, 0.00272089277474, 0.999993818823)-39.6305321481, 144.744965141, -0.400084960441
4given(-0.499984026115, -0.866032464122, -0.00193512699827), (0.866033887916, -0.499985269243, 0.000188470842206), (-0.00113075686114, -0.00158165314743, 0.999998109879)251.855261871, 68.4356890977, 0.190732031459
5given(0.50119271824, -0.865335498873, 0.000577558573678), (0.86533549691, 0.501192941572, 0.00033631281035), (-0.000580491693994, 0.00033122440375, 0.99999977666)145.427861735, -38.499894627, 0.0359890156072
6given(0.501044818325, 0.865420436194, 0.00124845815412), (-0.865420827664, 0.501045566926, -0.000361814486113), (-0.000938656074008, -0.000899156415581, 0.999999155221)-39.6492886472, 145.159175512, 0.241598482686
7given(-0.999996702519, 0.00220180462997, -0.00132174440634), (-0.00220280534189, -0.999997287949, 0.000756136825939), (-0.00132007595614, 0.000759045878231, 0.999998840624)211.944059299, 213.976423251, -0.000373915027581
8given(-0.501704388806, -0.865038864874, 0.000684478275839), (0.865038319862, -0.501702671873, 0.00177036876343), (-0.0011880332057, 0.00148030171613, 0.99999819864)251.654203875, 68.708226097, -0.14054400341
9given(-0.497928165181, 0.867214811718, -0.00245207197165), (-0.867216998788, -0.497930297283, -0.000309936285766), (-0.00148974226351, 0.00197215248997, 0.999996945637)66.4088616368, 252.034675063, -0.207456325269
10given(0.502057309094, -0.86482757019, -0.0034252334827), (0.864833401126, 0.502046942116, 0.0034722051045), (-0.00128323070771, -0.00470550227388, 0.999988105713)145.60056386, -39.0666976358, 0.970384847082
11given(-0.999999999997, -1.92838257177E-6, 1.29164451242E-6), (1.92838134486E-6, -0.999999999998, -9.49877275568E-7), (1.29164634415E-6, -9.49874784782E-7, 0.999999999999)212.220197065, 213.839878042, 4.56513198799E-6
12given(-0.50198848873, 0.864865758622, -0.00384405319022), (-0.86486874698, -0.501996235676, -0.00135272488629), (-0.00309962566622, 0.00264554914461, 0.999991696661)67.0933075783, 252.479685122, 0.0259021064535
13given(0.50076392042, 0.865578897903, 0.00294406358122), (-0.865569846998, 0.500772275618, -0.0039959905477), (-0.00493315051344, -0.00054724477092, 0.999987682199)-39.7592102238, 145.551984859, 0.469151711455
14given(-0.500958710232, -0.865470663008, -0.000949797724879), (0.865466849584, -0.500959372871, 0.00261514880803), (-0.00273914464536, 0.000488063129243, 0.999996129433)251.83000857, 68.4392073509, 0.247641937365
15given(0.497315143189, -0.867568932397, 0.00134010960275), (0.867560438661, 0.497316327365, 0.00391864860217), (-0.00406615617013, -0.000786177215882, 0.999991424113)145.895507904, -38.622745866, 0.390017605084
16given(0.498551654035, 0.866858060195, 0.00183077395843), (-0.866858294078, 0.498553746696, -0.000927169657843), (-0.0017164637074, -0.00112477962396, 0.999997894309)-39.6231084183, 145.739634014, 0.368240810136
17given(0.504869619985, -0.86319471291, 0.00124676379426), (0.863195077246, 0.504870389511, 0.000385244068935), (-0.000961994765921, 0.000881702343008, 0.999999148583)144.62047366, -38.9236582574, -0.0721608814205
18given(-0.491167222449, -0.871064942671, -0.000790722046675), (0.871062990786, -0.491167808042, 0.0018575321573), (-0.00200640835654, 0.000223590199452, 0.999997962164)251.69583362, 66.4221656763, 0.117838214075
19given(-0.502919854221, 0.864331944045, -0.00138229285045), (-0.864332477274, -0.50292071824, -0.000346257141965), (-0.000994464821819, 0.00102062101238, 0.999998984686)67.2816604151, 252.65474701, -0.0839006592805
20given(-0.999980199274, -0.00549988023519, -0.00305816584151), (0.00550317843872, -0.999984283737, -0.00107112378207), (-0.00305222672605, -0.00108793220536, 0.999994750144)213.398089811, 213.404624011, 0.425864342804
21given(0.499996166694, -0.866027615904, -4.22290771583E-5), (0.866027615443, 0.4999961681, -3.42985785864E-5), (5.08178930036E-5, -1.94223891776E-5, 0.99999999852)145.654400526, -38.4329822733, -0.00735552029243
22given(-0.500013780521, -0.866017447397, -9.65799905381E-6), (0.866017447342, -0.500013780249, -2.14458947115E-5), (1.37433863787E-5, -1.90872385784E-5, 0.999999999723)251.761635543, 68.4905694018, -0.00124561617361
23given(-0.999999999995, 4.05109543747E-7, 3.12713696598E-6), (-4.05096900818E-7, -0.999999999992, 4.04297220982E-6), (3.1271386038E-6, 4.042970943E-6, 0.999999999987)212.219822315, 213.840030109, -0.000883084374507
24given(-0.499997720581, 0.866026719346, 2.81626522305E-5), (-0.866026718788, -0.499997721305, 3.21609371883E-5), (4.19334928654E-5, -8.30921401769E-6, 0.999999999086)66.5665665428, 252.273026252, -0.00645580725248
25given(0.500014795318, 0.866016861534, 1.54610201032E-6), (-0.866016861418, 0.50001479522, 1.73478343743E-5), (1.42504431992E-5, -1.00131242643E-5, 0.999999999848)-39.5414106992, 145.349497918, -0.00176673323798
26given(-0.999981984843, -0.00556735659048, -0.00224377566601), (0.00556836691865, -0.999984397829, -0.000444285063222), (-0.00224126716486, -0.000456771225549, 0.999997384037)213.275630941, 213.536831792, 0.182057441642
27given(0.496740329195, -0.86789661041, -0.00212579144805), (0.867899030127, 0.496737140402, 0.00186731082571), (-0.00056467317122, -0.00277254093028, 0.999995997072)146.307602768, -38.2714240351, 0.47920784878
28given(0.495166820154, 0.868797708327, -0.000601850992681), (-0.868797904755, 0.495166809789, -0.000176571983966), (0.00014461130099, 0.000610319469245, 0.999999803299)-39.6622434636, 146.302654947, -0.145940775677
29given(-0.499266674083, -0.866439115576, 0.00400588947088), (0.866446481733, -0.499269914051, 0.000217290450558), (0.00181175114602, 0.00357937471882, 0.999991952785)251.536108569, 68.3297025147, -0.564132701402
30given(-0.504671364512, 0.863311521433, 0.000175506098633), (-0.863310003358, -0.504670072748, -0.00198891312993), (-0.00162847894464, -0.00115526367378, 0.999998006709)67.2652238048, 253.021220723, 0.242384008273

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Components

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Protein , 5 types, 30 molecules A1B1C1D1E1F1A3B3C3D3E3F3A4B4C4D4E4F4A6B6C6D6E6F6A7B7C7D7E7F7

#1: Protein
tail tube protein, gp7


Mass: 15665.332 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Vibrio phage XM1 (virus)
#3: Protein
baseplate organization protein, gp11


Mass: 27675.613 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Vibrio phage XM1 (virus)
#4: Protein
baseplate stabilizing protein, gp12


Mass: 13733.485 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Vibrio phage XM1 (virus)
#6: Protein
tail sheath protein, gp6


Mass: 53006.762 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Vibrio phage XM1 (virus)
#7: Protein
tail sheath initiator protein, gp15


Mass: 13392.063 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Vibrio phage XM1 (virus)

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Baseplate wedge protein, ... , 2 types, 18 molecules A2B2C2D2E2F2A5B5C5D5E5F5G5H5I5J5K5L5

#2: Protein
baseplate wedge protein, gp17


Mass: 27419.787 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Vibrio phage XM1 (virus)
#5: Protein
baseplate wedge protein, gp16


Mass: 44082.316 Da / Num. of mol.: 12 / 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
Molecular weightExperimental value: NO
Source (natural)Organism: Vibrio phage XM1 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Vibrio rotiferianus
Virus shellName: capsid / Diameter: 640 nm / Triangulation number (T number): 7
Buffer solutionpH: 7.5
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: 80 % / 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 / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 25 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: DIRECT ELECTRON DE-16 (4k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
EM software
IDNameCategory
1EMAN2particle selection
4CTFFINDCTF correction
9PHENIXmodel refinement
11jsprfinal Euler assignment
13jspr3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16068 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 114.9 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.009598910
ELECTRON MICROSCOPYf_angle_d0.9347134508
ELECTRON MICROSCOPYf_chiral_restr0.05415750
ELECTRON MICROSCOPYf_plane_restr0.005517598
ELECTRON MICROSCOPYf_dihedral_angle_d10.76913506
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2B1ELECTRON MICROSCOPYNCS constraints0.000694393022894
ens_1d_3C1ELECTRON MICROSCOPYNCS constraints0.0006911169827
ens_1d_4D1ELECTRON MICROSCOPYNCS constraints0.000708880230873
ens_1d_5A1ELECTRON MICROSCOPYNCS constraints0.000703867570836
ens_1d_6F1ELECTRON MICROSCOPYNCS constraints0.000706089274347
ens_2d_2A2ELECTRON MICROSCOPYNCS constraints0.000711227034052
ens_2d_3E2ELECTRON MICROSCOPYNCS constraints0.00069657712371
ens_2d_4D2ELECTRON MICROSCOPYNCS constraints0.000706670290573
ens_2d_5F2ELECTRON MICROSCOPYNCS constraints0.000707550725229
ens_2d_6C2ELECTRON MICROSCOPYNCS constraints0.000710295600912
ens_3d_2B3ELECTRON MICROSCOPYNCS constraints0.000424680357421
ens_3d_3C3ELECTRON MICROSCOPYNCS constraints0.000703022136274
ens_3d_4D3ELECTRON MICROSCOPYNCS constraints0.00070331816913
ens_3d_5A3ELECTRON MICROSCOPYNCS constraints0.000706744383148
ens_3d_6F3ELECTRON MICROSCOPYNCS constraints0.000707880342826
ens_4d_2A4ELECTRON MICROSCOPYNCS constraints0.000691933204684
ens_4d_3C4ELECTRON MICROSCOPYNCS constraints0.000694216767632
ens_4d_4D4ELECTRON MICROSCOPYNCS constraints0.000694985731837
ens_4d_5F4ELECTRON MICROSCOPYNCS constraints0.00070222918319
ens_4d_6E4ELECTRON MICROSCOPYNCS constraints0.000701122410811
ens_5d_2B6ELECTRON MICROSCOPYNCS constraints0.000712025446389
ens_5d_3C6ELECTRON MICROSCOPYNCS constraints0.000706246430749
ens_5d_4D6ELECTRON MICROSCOPYNCS constraints0.00047547179968
ens_5d_5E6ELECTRON MICROSCOPYNCS constraints0.00069957006379
ens_5d_6F6ELECTRON MICROSCOPYNCS constraints0.00070340744468
ens_6d_2E7ELECTRON MICROSCOPYNCS constraints0.000709324490223
ens_6d_3C7ELECTRON MICROSCOPYNCS constraints0.000729566592542
ens_6d_4A7ELECTRON MICROSCOPYNCS constraints0.000686906848093
ens_6d_5D7ELECTRON MICROSCOPYNCS constraints0.000715118830917
ens_6d_6F7ELECTRON MICROSCOPYNCS constraints0.000715820714918

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