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- PDB-9ygu: Flagella filament structure in H. pylori composed of flagellin FlaA -

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Basic information

Entry
Database: PDB / ID: 9ygu
TitleFlagella filament structure in H. pylori composed of flagellin FlaA
ComponentsFlagellin
KeywordsSTRUCTURAL PROTEIN / flagellin
Function / homology
Function and homology information


bacterial-type flagellum / structural molecule activity / extracellular region
Similarity search - Function
Flagellin hook, IN motif / Flagellin hook IN motif / Flagellin, C-terminal domain, subdomain 2 / Flagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region
Similarity search - Domain/homology
Chem-P8E / Flagellin
Similarity search - Component
Biological speciesHelicobacter pylori B128 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsKumar, R. / Yu, H. / Tachiyama, S. / Liu, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Office of the Director1S10 OD023603-01A1 United States
CitationJournal: PNAS Nexus / Year: 2026
Title: Assembly and glycosylation of sheathed flagella.
Authors: Rajeev Kumar / Shoichi Tachiyama / Huaxin Yu / Samira Heydari / Jiaqi Guo / Jack M Botting / Wangbiao Guo / Timothy R Hoover / Jun Liu /
Abstract: The bacterial flagellum is a complex nanomachine essential for motility, colonization, and invasion in diverse species. has evolved elaborate sheathed flagella that enable migration through the ...The bacterial flagellum is a complex nanomachine essential for motility, colonization, and invasion in diverse species. has evolved elaborate sheathed flagella that enable migration through the highly viscous gastric mucus layer to reach its colonization niche on the gastric epithelium, yet the molecular basis for these unique adaptations has remained elusive. Here, we use in situ single-particle cryo-electron microscopy to determine near-atomic structures of the flagellar filament within the membranous sheath of . The major flagellin FlaA constitutes the bulk of the filament, whereas the minor flagellin FlaB contributes critically to the hook-proximal region. Both FlaA and FlaB form a conserved core surrounded by variable surface-exposed domains. Our structures further reveal that pseudaminic acid glycans decorate these domains, where they mediate inter- and intra-subunit contacts that stabilize the filament and confer a negatively charged surface. Together, these findings support a model in which the filament rotates independently of the membranous sheath to drive motility and provide a molecular framework for understanding how the sheathed flagellum enables colonization and persistence within the gastric niche.
History
DepositionSep 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Y1: Flagellin
Q2: Flagellin
I3: Flagellin
R4: Flagellin
S5: Flagellin
g6: Flagellin
A7: Flagellin
e8: Flagellin
Z9: Flagellin
OA: Flagellin
FB: Flagellin
dC: Flagellin
JD: Flagellin
KE: Flagellin
LF: Flagellin
WG: Flagellin
UH: Flagellin
NI: Flagellin
BJ: Flagellin
fK: Flagellin
HL: Flagellin
XM: Flagellin
DN: Flagellin
MO: Flagellin
TP: Flagellin
GQ: Flagellin
VR: Flagellin
bS: Flagellin
CT: Flagellin
PU: Flagellin
cV: Flagellin
aW: Flagellin
EX: Flagellin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,809,047264
Polymers1,751,23933
Non-polymers57,808231
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "dC"
d_2ens_1chain "BJ"
d_3ens_1chain "CT"
d_4ens_1chain "DN"
d_5ens_1chain "EX"
d_6ens_1chain "FB"
d_7ens_1chain "GQ"
d_8ens_1chain "HL"
d_9ens_1chain "I3"
d_10ens_1chain "JD"
d_11ens_1chain "KE"
d_12ens_1chain "LF"
d_13ens_1chain "MO"
d_14ens_1chain "NI"
d_15ens_1chain "OA"
d_16ens_1chain "PU"
d_17ens_1chain "Q2"
d_18ens_1chain "R4"
d_19ens_1chain "S5"
d_20ens_1chain "TP"
d_21ens_1chain "UH"
d_22ens_1chain "VR"
d_23ens_1chain "WG"
d_24ens_1chain "XM"
d_25ens_1chain "Y1"
d_26ens_1chain "Z9"
d_27ens_1chain "aW"
d_28ens_1chain "bS"
d_29ens_1chain "cV"
d_30ens_1chain "A7"
d_31ens_1chain "e8"
d_32ens_1chain "fK"
d_33ens_1chain "g6"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ALAALALEULEUdCL2 - 5091 - 508
d_12P8EP8EP8EP8EdCGD601
d_13P8EP8EP8EP8EdCHD602
d_14P8EP8EP8EP8EdCID603
d_15P8EP8EP8EP8EdCJD604
d_16P8EP8EP8EP8EdCKD605
d_17P8EP8EP8EP8EdCLD606
d_18P8EP8EP8EP8EdCMD607
d_21ALAALALEULEUBJS2 - 5091 - 508
d_22P8EP8EP8EP8EBJDF601
d_23P8EP8EP8EP8EBJEF602
d_24P8EP8EP8EP8EBJFF603
d_25P8EP8EP8EP8EBJGF604
d_26P8EP8EP8EP8EBJHF605
d_27P8EP8EP8EP8EBJIF606
d_28P8EP8EP8EP8EBJJF607
d_31ALAALALEULEUCTCA2 - 5091 - 508
d_32P8EP8EP8EP8ECTVH601
d_33P8EP8EP8EP8ECTWH602
d_34P8EP8EP8EP8ECTXH603
d_35P8EP8EP8EP8ECTYH604
d_36P8EP8EP8EP8ECTZH605
d_37P8EP8EP8EP8ECTAI606
d_38P8EP8EP8EP8ECTBI607
d_41ALAALALEULEUDNW2 - 5091 - 508
d_42P8EP8EP8EP8EDNFG601
d_43P8EP8EP8EP8EDNGG602
d_44P8EP8EP8EP8EDNHG603
d_45P8EP8EP8EP8EDNIG604
d_46P8EP8EP8EP8EDNJG605
d_47P8EP8EP8EP8EDNKG606
d_48P8EP8EP8EP8EDNLG607
d_51ALAALALEULEUEXGA2 - 5091 - 508
d_52P8EP8EP8EP8EEXXI601
d_53P8EP8EP8EP8EEXYI602
d_54P8EP8EP8EP8EEXZI603
d_55P8EP8EP8EP8EEXAJ604
d_56P8EP8EP8EP8EEXBJ605
d_57P8EP8EP8EP8EEXCJ606
d_58P8EP8EP8EP8EEXDJ607
d_61ALAALALEULEUFBK2 - 5091 - 508
d_62P8EP8EP8EP8EFBZC601
d_63P8EP8EP8EP8EFBAD602
d_64P8EP8EP8EP8EFBBD603
d_65P8EP8EP8EP8EFBCD604
d_66P8EP8EP8EP8EFBDD605
d_67P8EP8EP8EP8EFBED606
d_68P8EP8EP8EP8EFBFD607
d_71ALAALALEULEUGQZ2 - 5091 - 508
d_72P8EP8EP8EP8EGQAH601
d_73P8EP8EP8EP8EGQBH602
d_74P8EP8EP8EP8EGQCH603
d_75P8EP8EP8EP8EGQDH604
d_76P8EP8EP8EP8EGQEH605
d_77P8EP8EP8EP8EGQFH606
d_78P8EP8EP8EP8EGQGH607
d_81ALAALALEULEUHLU2 - 5091 - 508
d_82P8EP8EP8EP8EHLRF601
d_83P8EP8EP8EP8EHLSF602
d_84P8EP8EP8EP8EHLTF603
d_85P8EP8EP8EP8EHLUF604
d_86P8EP8EP8EP8EHLVF605
d_87P8EP8EP8EP8EHLWF606
d_88P8EP8EP8EP8EHLXF607
d_91ALAALALEULEUI3C2 - 5091 - 508
d_92P8EP8EP8EP8EI3VA601
d_93P8EP8EP8EP8EI3WA602
d_94P8EP8EP8EP8EI3XA603
d_95P8EP8EP8EP8EI3YA604
d_96P8EP8EP8EP8EI3ZA605
d_97P8EP8EP8EP8EI3AB606
d_98P8EP8EP8EP8EI3BB607
d_101ALAALALEULEUJDM2 - 5091 - 508
d_102P8EP8EP8EP8EJDND601
d_103P8EP8EP8EP8EJDOD602
d_104P8EP8EP8EP8EJDPD603
d_105P8EP8EP8EP8EJDQD604
d_106P8EP8EP8EP8EJDRD605
d_107P8EP8EP8EP8EJDSD606
d_108P8EP8EP8EP8EJDTD607
d_111ALAALALEULEUKEN2 - 5091 - 508
d_112P8EP8EP8EP8EKEUD601
d_113P8EP8EP8EP8EKEVD602
d_114P8EP8EP8EP8EKEWD603
d_115P8EP8EP8EP8EKEXD604
d_116P8EP8EP8EP8EKEYD605
d_117P8EP8EP8EP8EKEZD606
d_118P8EP8EP8EP8EKEAE607
d_121ALAALALEULEULFO2 - 5091 - 508
d_122P8EP8EP8EP8ELFBE601
d_123P8EP8EP8EP8ELFCE602
d_124P8EP8EP8EP8ELFDE603
d_125P8EP8EP8EP8ELFEE604
d_126P8EP8EP8EP8ELFFE605
d_127P8EP8EP8EP8ELFGE606
d_128P8EP8EP8EP8ELFHE607
d_131ALAALALEULEUMOX2 - 5091 - 508
d_132P8EP8EP8EP8EMOMG601
d_133P8EP8EP8EP8EMONG602
d_134P8EP8EP8EP8EMOOG603
d_135P8EP8EP8EP8EMOPG604
d_136P8EP8EP8EP8EMOQG605
d_137P8EP8EP8EP8EMORG606
d_138P8EP8EP8EP8EMOSG607
d_141ALAALALEULEUNIR2 - 5091 - 508
d_142P8EP8EP8EP8ENIWE601
d_143P8EP8EP8EP8ENIXE602
d_144P8EP8EP8EP8ENIYE603
d_145P8EP8EP8EP8ENIZE604
d_146P8EP8EP8EP8ENIAF605
d_147P8EP8EP8EP8ENIBF606
d_148P8EP8EP8EP8ENICF607
d_151ALAALALEULEUOAJ2 - 5091 - 508
d_152P8EP8EP8EP8EOASC601
d_153P8EP8EP8EP8EOATC602
d_154P8EP8EP8EP8EOAUC603
d_155P8EP8EP8EP8EOAVC604
d_156P8EP8EP8EP8EOAWC605
d_157P8EP8EP8EP8EOAXC606
d_158P8EP8EP8EP8EOAYC607
d_161ALAALALEULEUPUDA2 - 5091 - 508
d_162P8EP8EP8EP8EPUCI601
d_163P8EP8EP8EP8EPUDI602
d_164P8EP8EP8EP8EPUEI603
d_165P8EP8EP8EP8EPUFI604
d_166P8EP8EP8EP8EPUGI605
d_167P8EP8EP8EP8EPUHI606
d_168P8EP8EP8EP8EPUII607
d_171ALAALALEULEUQ2B2 - 5091 - 508
d_172P8EP8EP8EP8EQ2OA601
d_173P8EP8EP8EP8EQ2PA602
d_174P8EP8EP8EP8EQ2QA603
d_175P8EP8EP8EP8EQ2RA604
d_176P8EP8EP8EP8EQ2SA605
d_177P8EP8EP8EP8EQ2TA606
d_178P8EP8EP8EP8EQ2UA607
d_181ALAALALEULEUR4D2 - 5091 - 508
d_182P8EP8EP8EP8ER4CB601
d_183P8EP8EP8EP8ER4DB602
d_184P8EP8EP8EP8ER4EB603
d_185P8EP8EP8EP8ER4FB604
d_186P8EP8EP8EP8ER4GB605
d_187P8EP8EP8EP8ER4HB606
d_188P8EP8EP8EP8ER4IB607
d_191ALAALALEULEUS5E2 - 5091 - 508
d_192P8EP8EP8EP8ES5JB601
d_193P8EP8EP8EP8ES5KB602
d_194P8EP8EP8EP8ES5LB603
d_195P8EP8EP8EP8ES5MB604
d_196P8EP8EP8EP8ES5NB605
d_197P8EP8EP8EP8ES5OB606
d_198P8EP8EP8EP8ES5PB607
d_201ALAALALEULEUTPY2 - 5091 - 508
d_202P8EP8EP8EP8ETPTG601
d_203P8EP8EP8EP8ETPUG602
d_204P8EP8EP8EP8ETPVG603
d_205P8EP8EP8EP8ETPWG604
d_206P8EP8EP8EP8ETPXG605
d_207P8EP8EP8EP8ETPYG606
d_208P8EP8EP8EP8ETPZG607
d_211ALAALALEULEUUHQ2 - 5091 - 508
d_212P8EP8EP8EP8EUHPE601
d_213P8EP8EP8EP8EUHQE602
d_214P8EP8EP8EP8EUHRE603
d_215P8EP8EP8EP8EUHSE604
d_216P8EP8EP8EP8EUHTE605
d_217P8EP8EP8EP8EUHUE606
d_218P8EP8EP8EP8EUHVE607
d_221ALAALALEULEUVRAA2 - 5091 - 508
d_222P8EP8EP8EP8EVRHH601
d_223P8EP8EP8EP8EVRIH602
d_224P8EP8EP8EP8EVRJH603
d_225P8EP8EP8EP8EVRKH604
d_226P8EP8EP8EP8EVRLH605
d_227P8EP8EP8EP8EVRMH606
d_228P8EP8EP8EP8EVRNH607
d_231ALAALALEULEUWGP2 - 5091 - 508
d_232P8EP8EP8EP8EWGIE601
d_233P8EP8EP8EP8EWGJE602
d_234P8EP8EP8EP8EWGKE603
d_235P8EP8EP8EP8EWGLE604
d_236P8EP8EP8EP8EWGME605
d_237P8EP8EP8EP8EWGNE606
d_238P8EP8EP8EP8EWGOE607
d_241ALAALALEULEUXMV2 - 5091 - 508
d_242P8EP8EP8EP8EXMYF601
d_243P8EP8EP8EP8EXMZF602
d_244P8EP8EP8EP8EXMAG603
d_245P8EP8EP8EP8EXMBG604
d_246P8EP8EP8EP8EXMCG605
d_247P8EP8EP8EP8EXMDG606
d_248P8EP8EP8EP8EXMEG607
d_251ALAALALEULEUY1A2 - 5091 - 508
d_252P8EP8EP8EP8EY1HA601
d_253P8EP8EP8EP8EY1IA602
d_254P8EP8EP8EP8EY1JA603
d_255P8EP8EP8EP8EY1KA604
d_256P8EP8EP8EP8EY1LA605
d_257P8EP8EP8EP8EY1MA606
d_258P8EP8EP8EP8EY1NA607
d_261ALAALALEULEUZ9I2 - 5091 - 508
d_262P8EP8EP8EP8EZ9LC601
d_263P8EP8EP8EP8EZ9MC602
d_264P8EP8EP8EP8EZ9NC603
d_265P8EP8EP8EP8EZ9OC604
d_266P8EP8EP8EP8EZ9PC605
d_267P8EP8EP8EP8EZ9QC606
d_268P8EP8EP8EP8EZ9RC607
d_271ALAALALEULEUaWFA2 - 5091 - 508
d_272P8EP8EP8EP8EaWQI601
d_273P8EP8EP8EP8EaWRI602
d_274P8EP8EP8EP8EaWSI603
d_275P8EP8EP8EP8EaWTI604
d_276P8EP8EP8EP8EaWUI605
d_277P8EP8EP8EP8EaWVI606
d_278P8EP8EP8EP8EaWWI607
d_281ALAALALEULEUbSBA2 - 5091 - 508
d_282P8EP8EP8EP8EbSOH601
d_283P8EP8EP8EP8EbSPH602
d_284P8EP8EP8EP8EbSQH603
d_285P8EP8EP8EP8EbSRH604
d_286P8EP8EP8EP8EbSSH605
d_287P8EP8EP8EP8EbSTH606
d_288P8EP8EP8EP8EbSUH607
d_291ALAALALEULEUcVEA2 - 5091 - 508
d_292P8EP8EP8EP8EcVJI601
d_293P8EP8EP8EP8EcVKI602
d_294P8EP8EP8EP8EcVLI603
d_295P8EP8EP8EP8EcVMI604
d_296P8EP8EP8EP8EcVNI605
d_297P8EP8EP8EP8EcVOI606
d_298P8EP8EP8EP8EcVPI607
d_301ALAALALEULEUA7G2 - 5091 - 508
d_302P8EP8EP8EP8EA7XB601
d_303P8EP8EP8EP8EA7YB602
d_304P8EP8EP8EP8EA7ZB603
d_305P8EP8EP8EP8EA7AC604
d_306P8EP8EP8EP8EA7BC605
d_307P8EP8EP8EP8EA7CC606
d_308P8EP8EP8EP8EA7DC607
d_311ALAALALEULEUe8H2 - 5091 - 508
d_312P8EP8EP8EP8Ee8EC601
d_313P8EP8EP8EP8Ee8FC602
d_314P8EP8EP8EP8Ee8GC603
d_315P8EP8EP8EP8Ee8HC604
d_316P8EP8EP8EP8Ee8IC605
d_317P8EP8EP8EP8Ee8JC606
d_318P8EP8EP8EP8Ee8KC607
d_321ALAALALEULEUfKT2 - 5091 - 508
d_322P8EP8EP8EP8EfKKF601
d_323P8EP8EP8EP8EfKLF602
d_324P8EP8EP8EP8EfKMF603
d_325P8EP8EP8EP8EfKNF604
d_326P8EP8EP8EP8EfKOF605
d_327P8EP8EP8EP8EfKPF606
d_328P8EP8EP8EP8EfKQF607
d_331ALAALALEULEUg6F2 - 5091 - 508
d_332P8EP8EP8EP8Eg6QB601
d_333P8EP8EP8EP8Eg6RB602
d_334P8EP8EP8EP8Eg6SB603
d_335P8EP8EP8EP8Eg6TB604
d_336P8EP8EP8EP8Eg6UB605
d_337P8EP8EP8EP8Eg6VB606
d_338P8EP8EP8EP8Eg6WB607

NCS oper:
IDCodeMatrixVector
1given(0.409432307732, -0.91234018901, -0.000751600346589), (0.912340490558, 0.409432055806, 0.000470070344512), (-0.000121134791911, -0.000878177414861, 0.999999607065)321.193897003, -68.8235904306, -46.6138654815
2given(0.402836303218, -0.915271862038, -0.000575648396887), (0.915272041525, 0.402836259306, 0.000195422357221), (5.30274621001E-5, -0.000605598103368, 0.999999815219)323.197968709, -67.9922517053, -98.2139608553
3given(-0.159257169492, -0.987237031386, -0.00044477553288), (0.987237090163, -0.159257016152, -0.000361404372117), (0.000285958155235, -0.000496655140202, 0.999999835781)458.5950537, 36.8314487386, -121.709566678
4given(-0.152211347968, -0.988347850504, -0.000481615209061), (0.988347966091, -0.152211300566, -0.000133806243004), (5.89398353139E-5, -0.000496370240928, 0.999999875071)457.316193921, 35.0470414824, -70.1476102129
5given(-0.144965002689, -0.989436621695, -0.000565371068973), (0.989436774618, -0.144965053122, 4.90516259563E-5), (-0.000130492522122, -0.000552288157859, 0.999999838975)456.029064255, 33.2184131778, -18.5835049944
6given(-0.659407091728, -0.751785949687, -0.000416211801034), (0.751786063066, -0.659406950387, -0.000434925407572), (5.25178561392E-5, -0.000599695129426, 0.999999818804)515.126305184, 193.979110789, -42.0296737156
7given(-0.664676592331, -0.747131101172, -0.000381141163205), (0.747131180124, -0.664676376791, -0.000560198003289), (0.000165205823667, -0.000657112946917, 0.999999770455)515.220434739, 196.114608153, -93.5486840625
8given(-0.670000625285, -0.742360529445, 8.02413892519E-5), (0.742360458241, -0.670000601956, -0.000378706760691), (0.000334898730471, -0.000194165731968, 0.999999925071)515.202675393, 198.210350304, -145.182568633
9given(-0.963960185564, -0.266046538354, 8.83362389332E-6), (0.266046477041, -0.963959984915, -0.00064771728606), (0.000180838201743, -0.000622023520747, 0.999999790192)476.32345775, 362.827987585, -116.970868147
10given(-0.962097545664, -0.272705520322, -0.000108690436342), (0.272705533011, -0.962097335362, -0.000639965158344), (6.99512523102E-5, -0.000645349391529, 0.999999789315)477.381562505, 361.018999285, -65.4325479983
11given(-0.960022220979, -0.279923773353, -0.000127818713171), (0.279923799966, -0.96002217395, -0.00030287992747), (-3.79255067199E-5, -0.000326550960558, 0.999999945963)478.476299743, 358.93967174, -13.9712416112
12given(-0.957933263382, 0.28699101438, 0.000143431350952), (-0.286991050145, -0.957933131944, -0.000501857828245), (-6.63104396644E-6, -0.000521909821198, 0.999999863783)356.878881536, 479.638614877, -37.3492218576
13given(-0.955833715815, 0.293907910419, 0.000218870380443), (-0.29390797035, -0.955833665918, -0.00032872745885), (0.000112588077572, -0.000378536537769, 0.999999922017)354.92865244, 480.594375802, -88.9080558078
14given(-0.953781059373, 0.300502133752, 0.000397986116987), (-0.300502251762, -0.953781064419, -0.000279003256561), (0.000295750548364, -0.000385703745936, 0.999999881882)353.04159541, 481.559912108, -140.457828982
15given(-0.643017874679, 0.765850915202, 0.000623320461037), (-0.765851154149, -0.643017808878, -0.000327345264746), (0.000150108486492, -0.000687859550913, 0.999999752158)187.214759504, 514.60450222, -112.267345597
16given(-0.648252095434, 0.761425581177, 0.000552353183959), (-0.761425781468, -0.648251933394, -0.000458439132026), (8.99673688096E-6, -0.000717760082708, 0.99999974237)189.289979438, 514.80197159, -60.7222707144
17given(-0.65375605306, 0.756705312263, 0.000305746016393), (-0.756705371861, -0.653755967219, -0.000339886576647), (-5.73106954456E-5, -0.000453562559866, 0.999999895498)191.534006776, 514.943956222, -9.25800995611
18given(-0.137911395745, 0.990444324884, 0.000697300412935), (-0.990444552991, -0.137911227365, -0.000284282004457), (-0.000185399942191, -0.00072984312381, 0.999999716478)31.3345937647, 454.684214608, -32.5768267618
19given(-0.130589414529, 0.991436348284, 0.000610012118776), (-0.991436535822, -0.130589399602, -6.44084767279E-5), (1.58042113751E-5, -0.000613199367115, 0.999999811868)29.5774606058, 453.283486346, -84.1567075221
20given(-0.123604484627, 0.992331477353, 0.000412836997124), (-0.992331518845, -0.123604592831, 0.000247665676272), (0.00029679499536, -0.000379058576116, 0.999999884114)27.9610651793, 451.887263184, -135.778286194
21given(0.429020130826, 0.903294822968, 0.000436057030461), (-0.903294875689, 0.429019891254, 0.000548144361956), (0.000308058824605, -0.000629053047001, 0.999999754696)-71.0498725282, 314.773912392, -107.637701012
22given(0.422860985749, 0.90619437089, 0.000590675931297), (-0.906194562982, 0.42286087598, 0.000305921088765), (2.74502268472E-5, -0.000664629410582, 0.999999778757)-70.4185170842, 316.753820627, -56.0580193456
23given(0.416136137036, 0.909302310225, 0.000155149286529), (-0.90930232205, 0.416136120825, 0.000126728464831), (5.06712635969E-5, -0.000193813900313, 0.999999979934)-69.5316386118, 318.901225247, -4.6545906176
24given(0.843485924129, 0.537151234932, 0.000215888412984), (-0.537151278313, 0.843485857438, 0.000335423568794), (-1.92563893385E-6, -0.000398889795906, 0.999999920442)-81.3587926695, 148.072529495, -28.0086980776
25given(0.847232141182, 0.531222761093, 0.000277570366899), (-0.531222832823, 0.84723199585, 0.000497086860806), (2.88973587633E-5, -0.000568599682046, 0.99999983793)-80.8759182448, 145.99363132, -79.4854304685
26given(0.850908132464, 0.525314524102, -2.95863223314E-5), (-0.525314463421, 0.850908058729, 0.000436017339674), (0.000254221481391, -0.000355468577184, 0.999999904507)-80.3164992947, 143.984290363, -131.085947901
27given(0.999893774587, -0.0145744217792, -0.000160535810166), (0.0145745058158, 0.999893642922, 0.000535373239275), (0.000152715980647, -0.000537656099131, 0.999999843802)3.17370504732, -3.22045868238, -102.934814763
28given(0.999971920289, -0.0074938652408, -2.48651570646E-5), (0.00749387867395, 0.999971744557, 0.000593186620134), (2.04191938947E-5, -0.000593356300095, 0.999999823756)1.61480234491, -1.74459819982, -51.3845269153
29given(0.415967226524, -0.909379602562, -7.00146561929E-5), (0.909379587194, 0.415967232374, -0.000167290034014), (0.000181253947407, 5.91727232772E-6, 0.999999983556)318.999670965, -69.4580295919, 4.62831363867
30given(0.839761223737, -0.542955776073, -0.000335166445573), (0.542955857122, 0.839760851777, 0.000805629303488), (-0.000155961423882, -0.00085851683451, 0.999999619312)150.282302883, -81.9011440213, -23.1960588462
31given(0.8354107573, -0.549625896086, -0.000490856000904), (0.549626109573, 0.835410544082, 0.000602090477212), (7.91417607192E-5, -0.000772780135668, 0.999999698274)152.692119566, -82.3743942943, -74.7784414697
32given(0.831647388953, -0.555303855483, -0.00049853120534), (0.555304039109, 0.831647335084, 0.000366328410324), (0.000211178569752, -0.000581492457893, 0.999999808635)154.691973488, -82.7215534108, -126.347991153

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Components

#1: Protein ...
Flagellin


Mass: 53067.848 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Source: (natural) Helicobacter pylori B128 (bacteria) / References: UniProt: B8Q9B9
#2: Sugar...
ChemComp-P8E / 5,7-diamino-3,5,7,9-tetradeoxy-L-glycero-alpha-L-manno-non-2-ulopyranosonic acid / Pse5Ac7Ac


Type: D-saccharide, beta linking / Mass: 250.249 Da / Num. of mol.: 231 / Source method: obtained synthetically / Formula: C9H18N2O6
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Flagella filament / Type: ORGANELLE OR CELLULAR COMPONENT / Details: Flagellin FlaA glycosylated with pseudaminic acid / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Helicobacter pylori (bacteria) / Strain: B120
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE / Humidity: 98 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 228410 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 83.64 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0011126852
ELECTRON MICROSCOPYf_angle_d0.3467171831
ELECTRON MICROSCOPYf_chiral_restr0.03521681
ELECTRON MICROSCOPYf_plane_restr0.001422209
ELECTRON MICROSCOPYf_dihedral_angle_d8.770419173
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2LdCELECTRON MICROSCOPYNCS constraints4.58542682229E-11
ens_1d_3LdCELECTRON MICROSCOPYNCS constraints1.13339418723E-12
ens_1d_4LdCELECTRON MICROSCOPYNCS constraints4.67153629317E-13
ens_1d_5LdCELECTRON MICROSCOPYNCS constraints3.28177628957E-11
ens_1d_6LdCELECTRON MICROSCOPYNCS constraints3.39939972302E-11
ens_1d_7LdCELECTRON MICROSCOPYNCS constraints7.45488738406E-12
ens_1d_8LdCELECTRON MICROSCOPYNCS constraints5.55191650919E-12
ens_1d_9LdCELECTRON MICROSCOPYNCS constraints4.25983873641E-12
ens_1d_10LdCELECTRON MICROSCOPYNCS constraints5.57908031709E-10
ens_1d_11LdCELECTRON MICROSCOPYNCS constraints2.75467163109E-12
ens_1d_12LdCELECTRON MICROSCOPYNCS constraints2.55661076709E-11
ens_1d_13LdCELECTRON MICROSCOPYNCS constraints6.2454254375E-12
ens_1d_14LdCELECTRON MICROSCOPYNCS constraints7.30055798996E-12
ens_1d_15LdCELECTRON MICROSCOPYNCS constraints8.15205103206E-12
ens_1d_16LdCELECTRON MICROSCOPYNCS constraints2.45421377872E-12
ens_1d_17LdCELECTRON MICROSCOPYNCS constraints1.33399265335E-12
ens_1d_18LdCELECTRON MICROSCOPYNCS constraints9.55843226316E-13
ens_1d_19LdCELECTRON MICROSCOPYNCS constraints4.69939800145E-13
ens_1d_20LdCELECTRON MICROSCOPYNCS constraints5.84240311725E-13
ens_1d_21LdCELECTRON MICROSCOPYNCS constraints3.99213788247E-13
ens_1d_22LdCELECTRON MICROSCOPYNCS constraints4.86953834079E-13
ens_1d_23LdCELECTRON MICROSCOPYNCS constraints6.45017434166E-13
ens_1d_24LdCELECTRON MICROSCOPYNCS constraints1.05408185461E-12
ens_1d_25LdCELECTRON MICROSCOPYNCS constraints7.87471614819E-13
ens_1d_26LdCELECTRON MICROSCOPYNCS constraints8.46644716426E-13
ens_1d_27LdCELECTRON MICROSCOPYNCS constraints3.32977887054E-10
ens_1d_28LdCELECTRON MICROSCOPYNCS constraints1.33740112666E-12
ens_1d_29LdCELECTRON MICROSCOPYNCS constraints6.38927169241E-13
ens_1d_30LdCELECTRON MICROSCOPYNCS constraints4.51542687241E-11
ens_1d_31LdCELECTRON MICROSCOPYNCS constraints3.36647235279E-12
ens_1d_32LdCELECTRON MICROSCOPYNCS constraints4.23033154757E-12
ens_1d_33LdCELECTRON MICROSCOPYNCS constraints4.91310382427E-12

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