[English] 日本語
Yorodumi
- PDB-9vpe: CryoEM structure of cyclised H-pilus (D69G) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9vpe
TitleCryoEM structure of cyclised H-pilus (D69G)
ComponentsPilin
KeywordsPROTEIN FIBRIL / pilus / conjugation / filament
Function / homology1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Pilin
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhi (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsIshimoto, N. / Beis, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Surface electrostatic potential affects mating pilus functionality
Authors: He, S. / Ishimoto, N. / Wong, J. / David, S. / Beis, K. / Frankel, G.
History
DepositionJul 3, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2672
Polymers7,5441
Non-polymers7231
Water00
1
A: Pilin
hetero molecules
x 104


Theoretical massNumber of molelcules
Total (without water)859,755208
Polymers784,566104
Non-polymers75,189104
Water0
TypeNameSymmetry operationNumber
point symmetry operation1_555x,y,z1
point symmetry operation103
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1generate(-0.162637, -0.986686), (0.986686, -0.162637), (1)327.93513, 26.84593, -110.34
2generate(-0.988652, -0.150226), (0.150226, -0.988652), (1)326.34136, 280.49972, -110.34
3generate(-0.448383, 0.893841), (-0.893841, -0.448383), (1)84.60977, 357.36728, -110.34
4generate(0.711536, 0.70265), (-0.70265, 0.711536), (1)-63.19479, 151.22026, -110.34
5generate(0.888136, -0.45958), (0.45958, 0.888136), (1)87.18855, -53.05317, -110.34
6generate(-0.620053, -0.78456), (0.78456, -0.620053), (1)366.88623, 127.47618, -98.08
7generate(-0.937768, 0.347263), (-0.347263, -0.937768), (1)242.67286, 348.64087, -98.08
8generate(0.040481, 0.99918), (-0.99918, 0.040481), (1)-6.0513, 298.85058, -98.08
9generate(0.962786, 0.270264), (-0.270264, 0.962786), (1)-35.55792, 46.9138, -98.08
10generate(0.554554, -0.832148), (0.832148, 0.554554), (1)194.93015, -59.00141, -98.08
11generate(-0.922403, -0.386228), (0.386228, -0.922403), (1)352.24175, 234.38349, -85.82
12generate(-0.652363, 0.757907), (-0.757907, -0.652363), (1)136.47257, 367.74932, -85.82
13generate(0.519221, 0.85464), (-0.85464, 0.519221), (1)-57.04221, 203.75294, -85.82
14generate(0.973259, -0.22971), (0.22971, 0.973259), (1)39.12825, -30.96822, -85.82
15generate(0.082286, -0.996609), (0.996609, 0.082286), (1)292.07965, -12.0375, -85.82
16generate(-0.994075, 0.108693), (-0.108693, -0.994075), (1)287.66405, 320.83205, -73.56
17generate(-0.203813, 0.97901), (-0.97901, -0.203813), (1)34.2995, 333.04634, -73.56
18generate(0.868112, 0.496368), (-0.496368, 0.868112), (1)-55.61094, 95.85676, -73.56
19generate(0.740335, -0.672238), (0.672238, 0.740335), (1)142.18591, -62.94875, -73.56
20generate(-0.41056, -0.911834), (0.911834, -0.41056), (1)354.34151, 76.09362, -73.56
21generate(-0.817145, 0.576432), (-0.576432, -0.817145), (1)189.30297, 365.20245, -61.3
22generate(0.295708, 0.955278), (-0.955278, 0.295708), (1)-38.2945, 253.21061, -61.3
23generate(0.999903, 0.013962), (-0.013962, 0.999903), (1)-2.11542, 2.14517, -61.3
24generate(0.322266, -0.946649), (0.946649, 0.322266), (1)247.84195, -41.02997, -61.3
25generate(-0.800731, -0.599024), (0.599024, -0.800731), (1)366.14503, 183.35177, -61.3
26generate(-0.43586, 0.900015), (-0.900015, -0.43586), (1)81.75706, 356.39836, -49.04
27generate(0.721277, 0.692647), (-0.692647, 0.721277), (1)-63.15483, 148.20776, -49.04
28generate(0.881633, -0.471935), (0.471935, 0.881633), (1)90.06596, -53.94607, -49.04
29generate(-0.176398, -0.984319), (0.984319, -0.176398), (1)329.67351, 29.30659, -49.04
30generate(-0.990653, -0.136407), (0.136407, -0.990653), (1)324.53833, 282.91339, -49.04
31generate(0.054427, 0.998518), (-0.998518, 0.054427), (1)-8.07815, 296.62154, -36.78
32generate(0.966466, 0.256795), (-0.256795, 0.966466), (1)-34.06431, 44.29734, -36.78
33generate(0.542881, -0.839809), (0.839809, 0.542881), (1)197.88011, -58.38943, -36.78
34generate(-0.630947, -0.775826), (0.775826, -0.630947), (1)367.21579, 130.47086, -36.78
35generate(-0.932828, 0.360322), (-0.360322, -0.932828), (1)239.92659, 349.87971, -36.78
36generate(0.531103, 0.847307), (-0.847307, 0.531103), (1)-57.73632, 200.82123, -24.52
37generate(0.969957, -0.243276), (0.243276, 0.969957), (1)41.70199, -32.53431, -24.52
38generate(0.068364, -0.99766), (0.99766, 0.068364), (1)294.36442, -10.07368, -24.52
39generate(-0.927706, -0.373312), (0.373312, -0.927706), (1)351.08008, 237.16328, -24.52
40generate(-0.641717, 0.766941), (-0.766941, -0.641717), (1)133.46986, 367.5035, -24.52
41generate(0.874958, 0.484199), (-0.484199, 0.874958), (1)-54.79872, 92.95555, -12.26
42generate(0.730877, -0.682509), (0.682509, 0.730877), (1)145.19611, -63.07281, -12.26
43generate(-0.423251, -0.906013), (0.906013, -0.423251), (1)355.3897, 78.91816, -12.26
44generate(-0.992461, 0.122562), (-0.122562, -0.992461), (1)285.30166, 322.70177, -12.26
45generate(-0.190124, 0.98176), (-0.98176, -0.190124), (1)31.79127, 331.37735, -12.26
47generate(0.309017, -0.951057), (0.951057, 0.309017), (1)250.53583, -39.68098
48generate(-0.809017, -0.587785), (0.587785, -0.809017), (1)365.69451, 186.33066
49generate(-0.809017, 0.587785), (-0.587785, -0.809017), (1)186.33066, 365.69451
50generate(0.309017, 0.951057), (-0.951057, 0.309017), (1)-39.68098, 250.53583
51generate(0.874958, -0.484199), (0.484199, 0.874958), (1)92.95555, -54.79872, 12.26
52generate(-0.190124, -0.98176), (0.98176, -0.190124), (1)331.37735, 31.79127, 12.26
53generate(-0.992461, -0.122562), (0.122562, -0.992461), (1)322.70177, 285.30166, 12.26
54generate(-0.423251, 0.906013), (-0.906013, -0.423251), (1)78.91816, 355.3897, 12.26
55generate(0.730877, 0.682509), (-0.682509, 0.730877), (1)-63.07281, 145.19611, 12.26
56generate(0.531103, -0.847307), (0.847307, 0.531103), (1)200.82123, -57.73632, 24.52
57generate(-0.641717, -0.766941), (0.766941, -0.641717), (1)367.5035, 133.46986, 24.52
58generate(-0.927706, 0.373312), (-0.373312, -0.927706), (1)237.16328, 351.08008, 24.52
59generate(0.068364, 0.99766), (-0.99766, 0.068364), (1)-10.07368, 294.36442, 24.52
60generate(0.969957, 0.243276), (-0.243276, 0.969957), (1)-32.53431, 41.70199, 24.52
61generate(0.054427, -0.998518), (0.998518, 0.054427), (1)296.62154, -8.07815, 36.78
62generate(-0.932828, -0.360322), (0.360322, -0.932828), (1)349.87971, 239.92659, 36.78
63generate(-0.630947, 0.775826), (-0.775826, -0.630947), (1)130.47086, 367.21579, 36.78
64generate(0.542881, 0.839809), (-0.839809, 0.542881), (1)-58.38943, 197.88011, 36.78
65generate(0.966466, -0.256795), (0.256795, 0.966466), (1)44.29734, -34.06431, 36.78
66generate(-0.43586, -0.900015), (0.900015, -0.43586), (1)356.39836, 81.75706, 49.04
67generate(-0.990653, 0.136407), (-0.136407, -0.990653), (1)282.91339, 324.53833, 49.04
68generate(-0.176398, 0.984319), (-0.984319, -0.176398), (1)29.30659, 329.67351, 49.04
69generate(0.881633, 0.471935), (-0.471935, 0.881633), (1)-53.94607, 90.06596, 49.04
70generate(0.721277, -0.692647), (0.692647, 0.721277), (1)148.20776, -63.15483, 49.04
71generate(-0.817145, -0.576432), (0.576432, -0.817145), (1)365.20245, 189.30297, 61.3
72generate(-0.800731, 0.599024), (-0.599024, -0.800731), (1)183.35177, 366.14503, 61.3
73generate(0.322266, 0.946649), (-0.946649, 0.322266), (1)-41.02997, 247.84195, 61.3
74generate(0.999903, -0.013962), (0.013962, 0.999903), (1)2.14517, -2.11542, 61.3
75generate(0.295708, -0.955278), (0.955278, 0.295708), (1)253.21061, -38.2945, 61.3
76generate(-0.994075, -0.108693), (0.108693, -0.994075), (1)320.83205, 287.66405, 73.56
77generate(-0.41056, 0.911834), (-0.911834, -0.41056), (1)76.09362, 354.34151, 73.56
78generate(0.740335, 0.672238), (-0.672238, 0.740335), (1)-62.94875, 142.18591, 73.56
79generate(0.868112, -0.496368), (0.496368, 0.868112), (1)95.85676, -55.61094, 73.56
80generate(-0.203813, -0.97901), (0.97901, -0.203813), (1)333.04634, 34.2995, 73.56
81generate(-0.922403, 0.386228), (-0.386228, -0.922403), (1)234.38349, 352.24175, 85.82
82generate(0.082286, 0.996609), (-0.996609, 0.082286), (1)-12.0375, 292.07965, 85.82
83generate(0.973259, 0.22971), (-0.22971, 0.973259), (1)-30.96822, 39.12825, 85.82
84generate(0.519221, -0.85464), (0.85464, 0.519221), (1)203.75294, -57.04221, 85.82
85generate(-0.652363, -0.757907), (0.757907, -0.652363), (1)367.74932, 136.47257, 85.82
86generate(-0.620053, 0.78456), (-0.78456, -0.620053), (1)127.47618, 366.88623, 98.08
87generate(0.554554, 0.832148), (-0.832148, 0.554554), (1)-59.00141, 194.93015, 98.08
88generate(0.962786, -0.270264), (0.270264, 0.962786), (1)46.9138, -35.55792, 98.08
89generate(0.040481, -0.99918), (0.99918, 0.040481), (1)298.85058, -6.0513, 98.08
90generate(-0.937768, -0.347263), (0.347263, -0.937768), (1)348.64087, 242.67286, 98.08
91generate(-0.162637, 0.986686), (-0.986686, -0.162637), (1)26.84593, 327.93513, 110.34
92generate(0.888136, 0.45958), (-0.45958, 0.888136), (1)-53.05317, 87.18855, 110.34
93generate(0.711536, -0.70265), (0.70265, 0.711536), (1)151.22026, -63.19479, 110.34
94generate(-0.448383, -0.893841), (0.893841, -0.448383), (1)357.36728, 84.60977, 110.34
95generate(-0.988652, 0.150226), (-0.150226, -0.988652), (1)280.49972, 326.34136, 110.34
96generate(0.335452, 0.942057), (-0.942057, 0.335452), (1)-42.34122, 245.12951, 122.6
97generate(0.99961, -0.027922), (0.027922, 0.99961), (1)4.31966, -4.20068, 122.6
98generate(0.282341, -0.959314), (0.959314, 0.282341), (1)255.86577, -36.87082, 122.6
99generate(-0.825113, -0.564967), (0.564967, -0.825113), (1)364.66893, 192.26812, 122.6
100generate(-0.79229, 0.610145), (-0.610145, -0.79229), (1)180.36688, 366.55391, 122.6
101generate(0.749649, 0.661835), (-0.661835, 0.749649), (1)-62.78267, 139.17772, 134.86
102generate(0.861097, -0.50844), (0.50844, 0.861097), (1)98.76904, -56.38257, 134.86
103generate(-0.217462, -0.976069), (0.976069, -0.217462), (1)334.68015, 36.83079, 134.86
104generate(-0.995496, -0.094803), (0.094803, -0.995496), (1)318.92952, 290.0001, 134.86
105generate(-0.397789, 0.917477), (-0.917477, -0.397789), (1)73.28399, 353.25398, 134.86

-
Components

#1: Protein Pilin


Mass: 7543.906 Da / Num. of mol.: 1 / Mutation: D69G
Source method: isolated from a genetically manipulated source
Details: The last five residues of AGIPL are cleaved when H-pilus make cyclisation.
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Gene: trhA, HCM1.67 / Production host: Escherichia coli (E. coli) / References: UniProt: Q935P5
#2: Chemical ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

-
Sample preparation

ComponentName: H-Pilus (D69G) / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 7.1 kDa/nm / Experimental value: NO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 46 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
8Cootmodel fitting
10PHENIX1.20.1_4487model refinement
11cryoSPARCinitial Euler assignment
12cryoSPARCfinal Euler assignment
14cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 28.96 ° / Axial rise/subunit: 12.26 Å / Axial symmetry: C5
3D reconstructionResolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 200984 / Num. of class averages: 1 / Symmetry type: HELICAL
RefinementHighest resolution: 3.11 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002551
ELECTRON MICROSCOPYf_angle_d0.33732
ELECTRON MICROSCOPYf_dihedral_angle_d12.254105
ELECTRON MICROSCOPYf_chiral_restr0.03380
ELECTRON MICROSCOPYf_plane_restr0.00284

+
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