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9ufe

Cryo-EM structure of the tubular mastigoneme (the central tube) from golden algae 2.17 angstrom resolution

Method: ELECTRON MICROSCOPY D_max: 210.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ufe
deposition_date	2025-04-10
title	Cryo-EM structure of the tubular mastigoneme (the central tube) from golden algae 2.17 angstrom resolution
keywords	Cryo-EM, Tubular Mastigoneme, Golden algae, N-Glycans, CARBOHYDRATE; CARBOHYDRATE
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	80.13 Å
rg_electron	80.44 Å
i0	13856800000.00
molecular_weight	937280.0 kDa
excluded_volume	1142500 Å³
envelope_volume	1960500 Å³
shell_volume	196010 Å³
envelope_diameter	274.1 Å
shell_rg	89.86 Å
envelope_rg	75.91 Å
shape_rg	80.46 Å
total_rg	80.44 Å
total_atoms	65299
n_residues	7632
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	210.5 Å
rg_real	79.56 Å
rg_real_error	0.80 Å
i0_real	1.3820e+10
i0_real_error	2.5210e+08
rg_reciprocal	80.93 Å
i0_reciprocal	13890000000.0000
total_estimate	0.8458
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	121.9 Å
skewness	-0.020
kurtosis	-0.790
angular_range	— – 0.0950 Å⁻¹
current_alpha	0.0124
highest_alpha	608500000.0000
n_real_points	20
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 1.000; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (25)

Entity 1 polymer

description	OCM5
formula_weight	40219.9 kDa
src_method	nat
entity_count	3

Polymer

type	polypeptide(L)
strand_id	EA,EB,EC
atom_count	71986

MFKLLIAFATIFGYAYAGCDNGCSGHGQCTQHGVCQCFDNWGIGLSHLSGDCSERICPYEIAWVDNPDKLGRRHQYAECANRGICNRESGECECFPGYEGKACQRSTCPNDCSGHGRCVYIQDLPFGAVAADYSTGDFSVQDPKTFDYNGWDRSKTRGCYCDPEYGDVDCSKRMCPYGTDVMDQRPDLTKPAKYQVQQIAIQAPTSTFGTSGLGGNTFALTFKSKLNETFTTLPIPLFNGASDFRTFILYVEQALERLPNGVIDNVDVAGSYSASSNVVYLNITFVGDSVQGPQHLLTVRDYLCGDGCTPKLEGVELLPYSNNITQLQKSDFSSYECGRRGKCDYATGICNCFAGYTGATCGTISCLV

Entity 2 polymer

description	OCM6
formula_weight	78780.8 kDa
src_method	nat
entity_count	3

Polymer

type	polypeptide(L)
strand_id	FA,FB,FC

MTKTLPVLTLLLLGIAGLINAECPNACSAHGKCGAYDMCTCFRNWMANDCSERICQFGLAHVDSPKGDLDASSGALSNASEIVVVNDFIYRFGTTELYPATTDIAGNVLTNTAHEYRECSNKGLCDRSTGTCSCFEGYEGSACQRASCPSGPNGVCSGHGTCETISEIAAQDFDNIYRLWDEDITMGCVCDSGYSGADCSQRDCPVGTDPLYFDNNATIRYSNFTYQFFSDSSSNVVTGNYSIIFTDVYGEDWNTVPIDIAATCATIQAALETLPNNVIDAGSVRCYKWNAAQSGPIVDGNMFIHARYTLAFPRNPGKLKQIAIDRFLDGSRATLYTNEPVSSLGWHVYPNGFTGEFVDLVPNRCFGVIANLAAGATLEGGVTGDIGTHYLAGLDATEQSLLKTCLGGSDNNTANNVEVYNWDYGSFNNPHLIKLQDATQYTYVYEVNSNGDIIYDPQIQYRPASSLCDSTSPNAARFGDDAYGNPMCWNKQAPGFYAVLVYVSSLANPFRLWTRAATDFGSTTPFYVYTTNGFLNLVSSDAGVYTYRNYYSNWEKVVSHHSNVVHSTNIGTTPGYYGDMSCETHPVGSTYALDCLNKGDLVMTLLQPDGSSATLANNPIYPNVYTTEKIYRARRNNITDVTYNEEERLNIIFDYSLNSAFSNRAPAYVYKFYPDTSSADGGYLHTGACGTRGICNSDTGLCECFSGYGKADCSCNTCNLLSF

Entity 3 polymer

description	Tubular mastigoneme protein
formula_weight	22290.1 kDa
src_method	nat
entity_count	3

Polymer

type	polypeptide(L)
strand_id	DA,DB,DC

MLRYILLLAFLLAVAQAACPNGCNGHGSCGANDKCTCYTRIDGEPAWTYADCSGRTCPKSSAWVGDVQNANDAHPVVECSNKGVCDRKTGECKCFANYDGIACERSICPNKCSDAGVCFTQKQLAVDAARTYATPWDAEKEVGCVCDLGRRGPDCSLFECPSGPDVLKGFGSEAGRDCSGRGLCDYSSGICNCFHGYYGTKCEYQTVLG

Entity 4 polymer

description	OCM3
formula_weight	36806.3 kDa
src_method	nat
entity_count	3

Polymer

type	polypeptide(L)
strand_id	CA,CB,CC

MKWLFLLSIVLMLSTKMTTVGSAPTEVPTGQPSGQPSGKPSGQPSGKPSGQPSGQPSGQPSGKPSGQPSGSPSGQPSGQPSGQPSGQPSGSPTGQPSGQPSRQPSGQPTARPSTQPSTQPSSSPSGQPTSVPSSAPSYRAESWGQITWDKRRHRQGGLCENHCSNHGTCEYNNNCKCFTGLDGEPEWTGPDCSLRTCPKDFAWVGEVVNANDLHPWAECSNKGVCDRTTGTCNCFAGYDGVACQRTVCPNNCNDRGTCWPEKLLASKAGRTYSEPWDAMKHVGCFCDAGYRGPACDLQECPSGTDPLDGYGNEAGRDCSGRGLCNYQEGTCQCFSGFYGTRCQYQTTIF

Entity 5 polymer

description	Tubular mastigoneme protein
formula_weight	83365.7 kDa
src_method	nat
entity_count	3

Polymer

type	polypeptide(L)
strand_id	AA,AB,AC

MKYSFLLSTTLVAALWSLAHSECANACNGHGKCTSYDMCICNRNWQASDCSERVCMFGLAHVDTPKGDLDGSGTLSNANIVVTENSFVYPYGTTEQFPQMQDSDLQTLTNTAHYYMECSNKGRCDRTTGECQCFDGYDGVACQRASCPGYPNSCSGHGVCKTISQLAESDYGNVYKLWDKDATMGCECDKGYTGADCSERLCKYGVDPLYLDDATTAKYSIFDLATLTTKTSSPYFTNGESEAKSAYWAIRFYDNHEEDWVTTPIIAGATCTEVVEALESLPNNVIPANSIDCSVVTFNGNENSFTMTNAYYDAQHPSGSRHPYRIFYRFAMWEALTASDQGELGPTTALQYYHGSNQTSTVSLYGNVYRLKFYSNPGKLKQPSIEVYLDGTRPSLISPGYKVITRVWTDGQQGEDDDYFADHCTGVTATIGVIASSTDYMTQSYLTGFTTTERGLLKKCLGDADFDTTNNVDVYNWDYGSKYYPHMIKLVRTVTSYNDGGYYAVLWYDSNTHWDSIAPEGTFRLLNPFRPPDNFLTDNYDIYTTKGTLALTSVFAEATFGFGSQYIYTVNTTYDQNSTISTVVYDGDISCEVGNNNAYKLDYISHCLNRSDLFTMLNWEFPEFNPPHLNLYSAKRLYTHSPEHYVVDRFAVNSVIARSNNTLHYMTHMITADLSTNWAASVGIDGGGHSSLTNPHFHVYKFFPATESTYEYVAECSNRGICDRDSGVCKCFAGYTSDSCSVQSSLSL

Entity 6 polymer

description	Tubular mastigoneme protein
formula_weight	40980.4 kDa
src_method	nat
entity_count	3

Polymer

type	polypeptide(L)
strand_id	BA,BB,BC

MFQARLLVLALCFAGIMAACDNNCSGHGTCSTDDVCECYDNWGVGLSHDSGDCSDRICPYELAWVDTPDNTGAFHKYAECANRGICNRETGECQCFDGYEGKGCQRSTCPNDCSGHGTCEYIEELAFGETWNDYSKQYFIEDPKTFPYHGWDNRKIRTCVCDPTYGDVDCSKRLCPYGNDVLDIQDNSIITNYQIQQIRIKAINQLQGLRTQTFALTFKSKLNETFTTYPIVFDDSDLNDFVHDVQLALLKLPNRVIDGVSVAANRDYATDYLNLNITFTGNNVQGKQNLLVVESYECSDGCTPKITGIDVQTLYNQKHSNISEVLAADYYSFECGRRGKCDYNTGLCNCFTGYTGDNCNTMTTLT

Entity 7 branched

description	;beta-D-xylopyranose-(1-2)-beta-D-xylopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)][2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)][beta-D-xylopyranose-(1-2)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)][alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	2362.1 kDa
src_method	man
entity_count	3

Entity 8 branched

description	;alpha-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-D-mannopyranose-(1-2)-beta-D-xylopyranose-(1-6)][beta-D-xylopyranose-(1-3)]alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[beta-D-xylopyranose-(1-3)]alpha-D-mannopyranose-(1-6)][beta-D-xylopyranose-(1-2)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	2656.4 kDa
src_method	man
entity_count	3

Entity 9 branched

description	;alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-D-xylopyranose-(1-2)-beta-D-xylopyranose-(1-6)][beta-D-glucopyranose-(1-3)]alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)][beta-D-xylopyranose-(1-2)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)][alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	2686.4 kDa
src_method	man
entity_count	3

Entity 10 branched

description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	1559.4 kDa
src_method	man
entity_count	3

Entity 11 branched

description	;beta-D-xylopyranose-(1-2)-beta-D-xylopyranose-(1-6)-[beta-D-xylopyranose-(1-3)][2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[beta-D-xylopyranose-(1-3)]alpha-D-mannopyranose-(1-6)][beta-D-xylopyranose-(1-2)]alpha-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-2)][alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	2464.2 kDa
src_method	man
entity_count	3

Entity 12 branched

description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	1559.4 kDa
src_method	man
entity_count	3

Entity 13 branched

description	;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	910.8 kDa
src_method	man
entity_count	3

Entity 14 branched

description	;beta-D-xylopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-[alpha-D-xylopyranose-(1-2)][alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-2)][alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	1661.5 kDa
src_method	man
entity_count	3

Entity 15 branched

description	alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-xylopyranose
formula_weight	636.6 kDa
src_method	man
entity_count	3

Entity 16 branched

description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-xylopyranose ;
formula_weight	1123.0 kDa
src_method	man
entity_count	3

Entity 17 branched

description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	1883.7 kDa
src_method	man
entity_count	9

Entity 18 branched

description	;alpha-D-xylopyranose-(1-2)-beta-D-xylopyranose-(1-6)-[beta-D-glucopyranose-(1-3)][2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[beta-D-xylopyranose-(1-3)]alpha-D-mannopyranose-(1-6)][beta-D-xylopyranose-(1-2)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	2332.1 kDa
src_method	man
entity_count	3

Entity 19 branched

description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	1721.5 kDa
src_method	man
entity_count	6

Entity 20 branched

description	;alpha-D-xylopyranose-(1-2)-beta-D-xylopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[alpha-D-xylopyranose-(1-3)]alpha-D-mannopyranose-(1-6)][beta-D-xylopyranose-(1-2)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)][alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	2332.1 kDa
src_method	man
entity_count	3

Entity 21 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	55

Entity 22 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	6

Entity 23 non-polymer

description	PHOSPHONATE
formula_weight	80.0 kDa
src_method	syn
entity_count	21

Entity 24 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	3

Entity 25 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	6687

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	2.17 Å
resolution_method	—
num_particles	104125

fit	/app/data/saxs_computation/uf/9ufe/9ufe.fit
pddf	/app/data/pr_computation/uf/9ufe/9ufe.pr.out
profile	/app/data/saxs_computation/uf/9ufe/9ufe.dat

Cryo-EM structure of the tubular mastigoneme (the central tube) from golden algae 2.17 angstrom resolution

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

EM 3D

5. Entities & Polymer Info (25)

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 branched

Entity 8 branched

Entity 9 branched

Entity 10 branched

Entity 11 branched

Entity 12 branched

Entity 13 branched

Entity 14 branched

Entity 15 branched

Entity 16 branched

Entity 17 branched

Entity 18 branched

Entity 19 branched

Entity 20 branched

Entity 21 non-polymer

Entity 22 non-polymer

Entity 23 non-polymer

Entity 24 non-polymer

Entity 25 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)