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9ya3

Cryo-EM structure of the apical region of subpellicular microtubule (SPMT) from Toxoplasma gondii (8-nm repeat)

Method: ELECTRON MICROSCOPY D_max: 338.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ya3
deposition_date	2025-09-15
title	Cryo-EM structure of the apical region of subpellicular microtubule (SPMT) from Toxoplasma gondii (8-nm repeat)
keywords	;Tubulin, Microtubule, Microtubule Inner Protein, Microtubule-associated Protein, Toxoplasma gondii, conoid, conoid fiber, subpellicular microtubule, SPMT, STRUCTURAL PROTEIN ;; STRUCTURAL PROTEIN
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	— Å
rg_electron	120.50 Å
i0	149597000000.00
molecular_weight	3251100.0 kDa
excluded_volume	4037400 Å³
envelope_volume	7064500 Å³
shell_volume	470050 Å³
envelope_diameter	372.6 Å
shell_rg	136.40 Å
envelope_rg	110.40 Å
shape_rg	120.50 Å
total_rg	120.60 Å
total_atoms	228257
n_residues	28883
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	338.1 Å
rg_real	121.20 Å
rg_real_error	1.15 Å
i0_real	1.4590e+11
i0_real_error	3.3570e+09
rg_reciprocal	127.20 Å
i0_reciprocal	152600000000.0000
total_estimate	0.8932
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	182.0 Å
skewness	-0.135
kurtosis	-0.721
angular_range	— – 0.0650 Å⁻¹
current_alpha	1.7570
highest_alpha	3476000000.0000
n_real_points	14
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.951; Stabil: 0.930; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (11)

Entity 1 polymer

description	Microtubule associated protein SPM1
formula_weight	38845.8 kDa
src_method	nat
entity_count	22

Polymer

type	polypeptide(L)
strand_id	0,1,10,11,12,13,14,15,16,17,18,19,2,22,23,3,4,5,6,7,8,9
atom_count	228257

MSGGNSNTPKKLPSEEGSDYGYPQKPQKYLPKSEQAEPDYSACCKGNDAYKGASHGTVQFSHPEEAQKYAGAAAGAETIQRGRERVAADRQPRAAGDVPARRLHLSDVDEAHRGQSPSRHPGYCVEELCTCGMHKCIPSRAPVPFTGSTQYRQEFVPKPLPPPTQVSQVTLPPSLPFEAESSYRTEFVAKPLPPPAKFSEVKLPPTLPFHGESAYRTDYVPKPLPEVAKPVEVKLPPTLPFNAQSCYRSEYVAKPLPPPVQTVEVKLPPSLPFEGSTHYRDEFQVKPLPPATKVTEVKLPPSLPFDATSMYRSDYVAKSNPICPVSKLPQYPAATYPQNHVFWDPDTKQWY

Entity 2 polymer

description	TLAP3 (apical cap protein AC5), TGME49_235380
formula_weight	65286.1 kDa
src_method	nat
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C

MPRPGVFELNYGEESRHSPVPKDPSTVTYGDASVGVVHHPLPAAGMYRQPCAFPHGSGFSKQSNETAFPDYPSTEHVAQRYVPPMDDKRQWAGHTSYYAPATMEQRGYQDARYFGAELMPKSQGGENPQNHPIMPSEAAEYGPRKPDCGRLIAAPHEGQVNNLSQVDGRICGTLPVIDNQSFQVEPCFRAPTIATGIPRLQTMKGRDAFAQDATRQRALQGHRTADLLKTPFDYDLFHRTRLPPSAGASIQAAGKEIDWSEKKLFRKAVVSTVFASDQVAERLRQDLPSPNTRDGQRTNADHGNRRNWSENIESLLRQATPVESSAENDPIFTAKVEERSFDSSLLYHGCRHLKKRSAFGHTPDAVAQLLRSSAEAGKGERPLVPSRPSRPSQHDSTQLKRVLSYHPDPEADSKGCFEQRARLRRSQLVTAKNSCRWGVNVFGYDLSPPRRNRLYALRDHLDSKLVPNQSTDDATHIKPRHTNVLSTSLHMSKLVPVTDLSPRPSFRYHADTGSLDATLLPVDAVPQERIGRRLISPPESSLQSNFVPSHEEVGRHKRFLVNSRDSLQGNMIPIVKECTRRRK

Entity 3 polymer

description	Tubulin alpha chain
formula_weight	50166.6 kDa
src_method	nat
entity_count	26

Polymer

type	polypeptide(L)
strand_id	A0,A2,A4,A6,A8,B0,B2,B4,B6,B8,C0,C2,C4,C6,C8,D0,D2,D4,D6,D8,E0,E2,E4,E6,E8,F0

MREVISIHVGQAGIQIGNACWELFCLEHGIQPDGQMPSDKTIGGGDDAFNTFFSETGAGKHVPRCVFLDLEPTVVDEVRTGTYRHLFHPEQLISGKEDAANNFARGHYTIGKEIVDLSLDRIRKLADNCTGLQGFLMFNAVGGGTGSGLGCLLLERLSVDYGKKSKLNFCSWPSPQVSTAVVEPYNSVLSTHSLLEHTDVAVMLDNEAIYDICRRNLDIERPTYTNLNRLIAQVISSLTASLRFDGALNVDVTEFQTNLVPYPRIHFMLSSYAPIISAEKAYHEQLSVAEITNSAFEPASMMAKCDPRHGKYMACCLMYRGDVVPKDVNAAVATIKTKRTIQFVDWCPTGFKCGINYQPPTVVPGGDLAKVMRAVCMISNSTAIAEVFSRMDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDLAALEKDYEEVGIETAEGEGEEEGYGDEY

Entity 4 polymer

description	Tubulin beta chain
formula_weight	50119.1 kDa
src_method	nat
entity_count	26

Polymer

type	polypeptide(L)
strand_id	A1,A3,A5,A7,A9,B1,B3,B5,B7,B9,C1,C3,C5,C7,C9,D1,D3,D5,D7,D9,E1,E3,E5,E7,E9,F1

MREIVHVQGGQCGNQIGAKFWEVISDEHGIDPTGTYCGDSDLQLERINVFYNEATGGRFVPRAILMDLEPGTMDSVRAGPFGQLFRPDNFVFGQTGAGNNWAKGHYTEGAELIDSVLDVVRKEAEGCDCLQGFQITHSLGGGTGSGMGTLLISKVREEYPDRIMETFSVFPSPKVSDTVVEPYNATLSVHQLVENADEVQVIDNEALYDICFRTLKLTTPTYGDLNHLVSAAMSGVTCCLRFPGQLNSDLRKLAVNLIPFPRLHFFLIGFAPLTSRGSQQYRALSVPELTQQMFDAKNMMCASDPRHGRYLTASAMFRGRMSTKEVDEQMLNVQNKNSSYFVEWIPNNMKSSVCDIPPKGLKMSVTFVGNSTAIQEMFKRVSDQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATAEEEGEFDEEEGEMGAEEGA

Entity 5 polymer

description	TLAP4 (thioredoxin-like associated protein), TGME49_201760
formula_weight	37360.2 kDa
src_method	nat
entity_count	3

Polymer

type	polypeptide(L)
strand_id	E,F,G

MERSGHLCKMEPWKQKVPQCLSLHGSNSLRGGKRTYNCNVLMDNWRNDRLDAHNDQKLTSWRIPHPLYTELPQGSKYETHYRQSYDYEDWARRPVRLSKYGLLGHDDSGAESWTTETRSEYEPPRLRRDQLKAAGQWPYGEDIYPRHVHGNEEFMCPHPMAIHVSRTHREDYIRSLTPRPAYERPPAGVPSSSGRLPGVPPYANDPISHHGGSQEQRHFCRMPCRNPSGSSSVQGTTGVDARASPAGSPVFAGQVPAQVKQEGGECGQGYAGIAATEDGLVDHGNSQTDRSAGQHCMLNASGGSERAHAAANTSTCPQRKESDPQPTVSWAAVPCQ

Entity 6 polymer

description	TLAP2 (thioredoxin-like associated protein), TGME49_232130
formula_weight	47924.4 kDa
src_method	nat
entity_count	4

Polymer

type	polypeptide(L)
strand_id	H,I,J,K

MDPRGQPVGPARPGVPPQMMRPQGGPPPGAFPGGPRGPAGAPFGAPMGPGGPMGPPRGPGPQMGPPRGPGPQMGPPRGQQGPPPPGVRGLMPGMTPQGPPGARPGMPPPGTMPMGPDGKLRMQPQTAPGAPPAGMPGTGMPPQQVPRGPMGHVGGGTGGMPAPDARQPVPSKTDSHGLQQKDLAQRSRNLRTLEDDERSDHQFGEEILNKGLQTFARLVALNDVGDLGAWNGYTWKSRRPPSVFFINITHDPEGRLWAVTESNEVGKLTVKGFKAIGHIGQEDVVDITFDPKDGTLWAINRVGELLHWNGYTWDKKYHAGFHKLRAATFDRKGNLWVVNTAGEIAMWDEEEQQWDLKKVPGATRLHTLAFDENNKLWVLGSHGELMLLAANRWVVYGWVGCWKFRDISFRWSKTAIEQLRAVRSTGTVFGGRSSALADRLPVPQGA

Entity 7 polymer

description	TRXL1, TGME49_232410
formula_weight	24939.3 kDa
src_method	nat
entity_count	22

Polymer

type	polypeptide(L)
strand_id	a,b,c,d,e,f,g,h,i,j,m,n,o,p,q,r,s,t,u,v,w,x

MSQPVFASPLNVEKRRLNEERALMQAQKAGGEGVNIQLPPNYGDMDLILFPEGSLKNSNNTVIPQSHLKGKSVALYFADGADPKCASLLPFLLNYYRTMNEGGANQKIEIIFVSLDRDREAFESHRAHMPWLSIDLENPLTEILKRHFRVMKEYEVPTYGYGSRTGVPSVIVIGSDGREAQFLPICSGLEEGDRALLRWDWRNTKFASDQFHVRPTLLEQ

Entity 8 polymer

description	TRXL2, TGME49_225790
formula_weight	21687.9 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	k,l

MLAADCFFGPDVVKRTQQGNYVPVRPDHFAGVSVALFFAKAGHSKCAQIVPVVRQFYKTTNFSGEKAVIEIIYVSLDKDEQDFERVRALMPWCSVEYKSCLRKKLIERYRVPNGELAFGTVRIPSTAIPLLIVIGPNGEEAGRMNFQQSDEFVLQRWDYRFNKWPGSAQRLRTLNDATDPWKKRLPQNV

Entity 9 non-polymer

description	GUANOSINE-5'-DIPHOSPHATE
formula_weight	443.2 kDa
src_method	syn
entity_count	26

Entity 10 non-polymer

description	GUANOSINE-5'-TRIPHOSPHATE
formula_weight	523.2 kDa
src_method	syn
entity_count	26

Entity 11 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	26

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6. Citations (1)

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resolution	3.30 Å
resolution_method	—
num_particles	225207

fit	/app/data/saxs_computation/ya/9ya3/9ya3.fit
pddf	/app/data/pr_computation/ya/9ya3/9ya3.pr.out
profile	/app/data/saxs_computation/ya/9ya3/9ya3.dat

Cryo-EM structure of the apical region of subpellicular microtubule (SPMT) from Toxoplasma gondii (8-nm repeat)

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

EM 3D

5. Entities & Polymer Info (11)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Entity 6 polymer

Polymer

Entity 7 polymer

Polymer

Entity 8 polymer

Polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)