← Back to search

9sfp

Native cytoplasmic lattices from mouse oocytes

Method: ELECTRON MICROSCOPY D_max: 297.2 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9sfp
deposition_date	2025-08-20
title	Native cytoplasmic lattices from mouse oocytes
keywords	oocyte, embryo, cytoskeleton, tubulin, ubiquitin, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	— Å
rg_electron	110.20 Å
i0	37012500000.00
molecular_weight	1673100.0 kDa
excluded_volume	2104800 Å³
envelope_volume	3584800 Å³
shell_volume	277380 Å³
envelope_diameter	406.0 Å
shell_rg	97.61 Å
envelope_rg	107.40 Å
shape_rg	110.10 Å
total_rg	110.20 Å
total_atoms	117354
n_residues	14769
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

▼

3. P(r) Analysis (GNOM)

dmax	297.2 Å
rg_real	104.60 Å
rg_real_error	1.07 Å
i0_real	3.5390e+10
i0_real_error	7.1110e+08
rg_reciprocal	104.80 Å
i0_reciprocal	36410000000.0000
total_estimate	0.9132
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	106.1 Å
skewness	0.290
kurtosis	-0.566
angular_range	— – 0.0700 Å⁻¹
current_alpha	0.9832
highest_alpha	1202000000.0000
n_real_points	15
gnom_version	4.1.3
quality_criteria	AN1: 0.003; Oscil: 1.000; Stabil: 0.973; Sysdev: 1.000; Positv: 1.000; Valcen: 0.952; Smooth: 0.000

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (13)

Entity 1 polymer

description	F-box and WD-40 domain protein 12
formula_weight	54036.7 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	117354

MEVHLPRLPLMKIFSYLDAYSLLQAAQVNKNWNELASSDVLWRKLCQKRWLFCDMVTLQLLGTETWKQFFVFRTWQEHAKTRAKPEDFTYKEIPAEYGFRANACYISGCGLTRNVQDRSVICMVSSMTKLSTWDIREGIMTWVSTEQPAYIKLLTTLPEMHIAVTVDTHSTIKLWDCHNREALATNCLFSSCKLLKAVFSKDDPIVLVGDISGNLYIFRIPDLHLISKVNVFPYGIDELHCSPQKKWVFLIMKHPRVLTKVVYMNSLLRTSEFSAPVSTILKFSLCDKAFWTPRREDRITQMSRGVPPRPTKFATFDMKLEEIGNKVTVQEYLVASFSLQDYEASPEWMGVSNKDVIVCSTGSSLLLFNIHGLRLQTFHYCPEEILRLWVDPLHVIVTCNDGSMDVYAWEERSLLLRKCYRLQNRRNLPPESFIFKTLCDDVSIIGVMTNSPAPCFLMAYTLASALEN

Entity 2 polymer

description	KH domain-containing protein 3
formula_weight	48055.3 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MASLKRFQTLVPLDHKQGTLFEIIGEPKLPKWFHVECLEDPKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWGPERRAEIWIFGPPPFRRDVDRMLTDLAHYCRMKLMEIEALEAGVERRRMAAHKAATQPAPVKVREAAPRPASVKVPETATQPAPVKVREAAPQPAPVQEVREAAPQQASVQEEVREAATEQAPVQEVREAATEQAPVQEVSEAATEQAPVQEVNEAATEQASVQAVREAATRPAPGKVRKAATQPAPVQVCQEATQLAPVKVREAATQPASGKVREAATQLAPVKVRKAATQLAPVKVHEAATQPAPGKVSDAATQSASVQVREAATQLSPVEATDTSQLAQVKADEAFAQHTSGEAHQVANGQSPIEVCETATGQHSLDVSRALSQKCPEVFEWETQSCLDGSYVIVQPPRDAWESFIIL

Entity 3 polymer

description	NLR family, pyrin domain containing 4F
formula_weight	108001.3 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,F

MASFISDFGLIWYLRELNKKEFMKFKDFLIQEILELKLKQVSSTKVKKASREDLANLLLKCGENQAWDMTFRILQKINRKDLTERATGAIVGNPNLYRDHLKKKLTHDCPKKFNVRIQDFIKETFIQNDYDAFENLLISKGTERKPHMVFLKGMAGVGKTLMLKNLMLAWSKGLVFQNKFSYAFYFCCQDVKQLKTASLAELISREWPSPSAPIEEILSQPEKLLFIIDSLEGMEWDLTKQESELCDDCMEKQPVSTLLSSLLRRKMLPESSLLLSTTPETFEKMEDRIQCTDVKTATAFDERSMKIYFHRLFQDRKRAQEAFSLVRENKQLFTICQVPLLCWMVATCLKEEIEKGGDPVSLCRRTTSLYTTHIFSLFIPQSAQYPSKKSQDQLQGLCSLAAEGMWTDTFVFGKEALRRNGIFDSDIPTLLDIGMLGKIREFENSYIFLHPSVQEVCAAIFYMLKRHVEHPSQDVKNIETVLFMFLKKVKTQWIFLGCFIFGLLQKSEQEKLGVFFGHRLSKNIHHKLYQCLETLSGNAELQEQIDGMRLFSCLFEMEDEAFLVKAMNCMQQINFVAKNYSDFIVAAYCLKHCSTLKKLSFSTENVLNEGDQSYMEELLICWNNMCSVFVRSKDIQELRIKDTNFNEPAIRVLYESLKYPSFTLNKLVANNVSFGDNHVLFELIQNSSLQYLDLSCSFLSHNEVKLLCDILNQAECNIEKLMIAHCKLSPDDCKIFGSILMSSKSLKVLNLASNNLNQGISSLCKALCHPHCTLEYLVLSNCSLSEQCWDYLSEVLRQNKTLSHLDISSNDLKDEGLKILCRSLILPYCVLESLCLSCCGITERGCQDLAEVLKNNQNLKYLHVSYNKLKDTGVMLLCDAIKHPNCHLKDLQLEACEITDASNEELCYAFMQCETLQTLNLMGNAFEVSRMVFFPRF

Entity 4 polymer

description	NACHT, LRR and PYD domains-containing protein 5
formula_weight	131468.5 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	H,I

MGPPEKESKAILKARGLEEEQKSERKMTSPENDSKSIQKDQGPEQEQTSESTMGPPEKESKAILKARGLEEEQKSERKMTSPENDSKSIQKDQGPEQEQTSESTMGPPEKDSKAILKARGLEEEQKSESTMSPSENVSRAILKDSGSEEVEQASERKMTSPENDSKSIQKDQGPEQEQTSETLQSKEEDEVTEADKDNGGDLQDYKAHVIAKFDTSVDLHYDSPEMKLLSDAFKPYQKTFQPHTIILHGRPGVGKSALARSIVLGWAQGKLFQKMSFVIFFSVREIKWTEKSSLAQLIAKECPDSWDLVTKIMSQPERLLFVIDGLDDMDSVLQHDDMTLSRDWKDEQPIYILMYSLLRKALLPQSFLIITTRNTGLEKLKSMVVSPLYILVEGLSASRRSQLVLENISNESDRIQVFHSLIENHQLFDQCQAPSVCSLVCEALQLQKKLGKRCTLPCQTLTGLYATLVFHQLTLKRPSQSALSQEEQITLVGLCMMAAEGVWTMRSVFYDDDLKNYSLKESEILALFHMNILLQVGHNSEQCYVFSHLSLQDFFAALYYVLEGLEEWNQHFCFIENQRSIMEVKRTDDTRLLGMKRFLFGLMNKDILKTLEVLFEYPVIPTVEQKLQHWVSLIAQQVNGTSPMDTLDAFYCLFESQDEEFVGGALKRFQEVWLLINQKMDLKVSSYCLKHCQNLKAIRVDIRDLLSVDNTLELCPVVTVQETQCKPLLMEWWGNFCSVLGSLRNLKELDLGDSILSQRAMKILCLELRNQSCRIQKLTFKSAEVVSGLKHLWKLLFSNQNLKYLNLGNTPMKDDDMKLACEALKHPKCSVETLRLDSCELTIIGYEMISTLLISTTRLKCLSLAKNRVGVKSMISLGNALSSSMCLLQKLILDNCGLTPASCHLLVSALFSNQNLTHLCLSNNSLGTEGVQQLCQFLRNPECALQRLILNHCNIVDDAYGFLAMRLANNTKLTHLSLTMNPVGDGAMKLLCEALKEPTCYLQELELVDCQLTQNCCEDLACMITTTKHLKSLDLGNNALGDKGVITLCEGLKQSSSSLRRLGLGACKLTSNCCEALSLAISCNPHLNSLNLVKNDFSTSGMLKLCSAFQCPVSNLGIIGLWKQEYYARVRRQLEEVEFVKPHVVIDGDWYASDEDDRNWWKN

Entity 5 polymer

description	NACHT, LRR and PYD domains-containing protein 14
formula_weight	113527.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	J

MKTEDDEMEYEASKEETVSEDKDFDDGIDYRTVIKENIFTMWYKTSLHGEFATLNCVITPKDQNLLQHIFDEDIQTSEAPQTVVLQGAAGIGKTTLLKKAVLEWADGNLYQQFTHVFYLNGKEISQVKEKSFAQLISKHWPSSEGPIEQVLSKPSSLLFIIDSFDELDFSFEEPQFALCKDWTQISPVSFLISSLLRKVMLPESYLLVATRSTAWKRLVPLLQKPQRVKLSGLSKNARMDYIHHLLKDKAWATSAIYSLRMNWRLFHMCHVCHMCQMICAVLKGQVEKGGRVEETCKTSTALFTYYICSLFPRIPVGCVTLPNETLLRSLCKAAVEGIWTMKHVLYQQNLRKHELTREDILLFLDAKVLQQDTEYENCYMFTHLHVQEFFAALFYLLRENLEEQDYPSEPFENLYLLLESNHIHDPHLEQMKCFLFGLLNKDRVRQLEETFNLTISMEVREELLACLEGLEKDDSSLSQLRFQDLLHCIYETQDQEFITQALMYFQKIIVRVDEEPQLRIYSFCLKHCHTLKTMRLTARADLKNMLDTAEMCLEGAAVQVIHYWQDLFSVLHTNESLIEMDLYESRLDESLMKILNEELSHPKCKLQKLIFRAVDFLNGCQDFTFLASNKKVTHLDLKETDLGVNGLKTLCEALKCKGCKLRVLRLASCDLNVARCQKLSNALQTNRSLVFLNLSLNNLSNDGVKSLCEVLENPNSSLERLALASCGLTKAGCKVLSSALTKSKRLTHLCLSDNVLEDEGIKLLSHTLKHPQCTLQSLVLRSCSFTPIGSEHLSTALLHNRSLVHLDLGQNKLADNGVKLLCHSLQQPHCNLQELELMSCVLTSKACGDLASVLVNNSNLWSLDLGHNILDDAGLNILCDALRNPNCHVQRLGLENCGLTPGCCQDLLGILSNNKSVIQMNLMKNALDHESIKNLCKVLRSPTCKMEFLALDKKEILKKKIKKFLVDVRINNPHLVIGPECPNTESGCWWNYF

Entity 6 polymer

description	Oocyte-expressed protein homolog
formula_weight	18481.3 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	K,L

MASHTADADAKPDSDSQKLLNVLPVSLRLRTRPWWFPIQEVSNPLVLYMEAWVAERVIGTDQAEISEIEWMCQALLTVDSVNSGNLAEITIFGQPSAQTRMKNILLNMAAWHKENELQRAVKVKEVEEFLKIRASSILSKLSKKGLKLAGFPLPLEGRETQMES

Entity 7 polymer

description	Inactive protein-arginine deiminase type-6
formula_weight	76854.1 kDa
src_method	nat
entity_count	10

Polymer

type	polypeptide(L)
strand_id	M,N,O,P,Q,R,S,T,U,V

MSFQNSLSLSLVNPTHALCMVGMEITLDISKCAPDKCKSFTIRGSPRILIHISSSVIAGKEDTVVWRSMNHPTVALVRMVAPSPTVDEDKVLVSYFCPDQEVPTATAVLFLTGIEISLEADIYRDGQLDMPSDKQAKKKWMWGMNGWGAILLVNCSPNAVGQPDEQSFQEGPREIQNLSQMNVTVEGPTSILQNYQLILHTSEEEAKKTRVYWSQRGSSAYELVVGPNKPVYLLPTFENRRKEAFYVEATEFPSPSFSGLISLSLSLVEKAHDECIPEIPLYKDTVMFRVAPYIFMPSTQMPLEVYLCRELQLQGFVDSVTKLSEKSKVQVVKVYEDPNRQSKWLQDEMAFCYTQAPHKTVSLILDTPRVSKLEDFPMKYTLTPGSGYLIRQTEDHRVASLDSIGNLMVSPPVKAQGKDYPLGRVLIGGSFYPSSEGRDMNKGLREFVYAQQVQAPVELFSDWLMTGHMDQFMCFVPTNDKNNDQKDFRLLLASPSACFELFEQKQKEGYGNVTLFEDIGAEQLLSNGRESKTISQILADKSFREQNTYVEKCISLNRTLLKTELGLEDKDIILIPQLFCLEQLTNVPSNQQSTKLFARPYFPDMLQIIVLGKNLGIPKPFGPKINGTCCLEEKVCGLLEPLGLKCTFIDDFDCYLANIGDVCASAIINRVPFAFKWWKMTP

Entity 8 polymer

description	Transducin-like enhancer protein 6
formula_weight	65187.3 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	W,Y

MTSHRQSSDTFGGILPSTLSSRYLSIVNQLPEEFSSVVSEMMVHLENIFSLAENFFQAIERFSRTPDLLERNKMSIGVGAEGDSWPCHVSHEAPMGSAQTTENSAKEEDKQVPESAALQHPKFKSTPGPQLPTRRRFLSESDELQDPQPVWDAEPQFCQGFLIQGLWELFMDSRQKNQQEHGGEDSSQESKDSGLCDFKPEPQPRHRNSLSDSADPFLIKSPSALLDYYQEDVSRPQPETQESSGRADKFLKPLSWGSEVLESSCNQPSTALWQLERFTVPQALQKVRVLKHQELLLVVAVSSFTRHVFTCSQSGIKVWNLVNQVAEDRDPESHLKCSVQDNKVYLRTCLLSSNSRTLFAGGYNLPGVIVWDLAAPSLYEKCQLPCEGLSCQALANTKENMALAGFTDGTVRIWDLRTQEIVRNLKGPTNSARNLVVKDDNIWTGGLDACLRCWDLRMAKVSLEHLFQSQIMSLAHSPTEDWLLLGLANGQHCLFNSRKRDQVLTVDTKDNTILGLKFSPNGKWWASVGMGNFITVHSMPTGAKLFQVPEVGPVRCFDMTENGRLIITGSRDCASVYHIKY

Entity 9 polymer

description	Tubulin alpha-1A chain
formula_weight	50188.4 kDa
ec_number	3.6.5.-
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	a

MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Entity 10 polymer

description	Tubulin beta-4B chain
formula_weight	49877.8 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	b

MREIVHLQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLERINVYYNEATGGKYVPRAVLVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATAEEEGEFEEEAEEEVA

Entity 11 polymer

description	Ubiquitin-conjugating enzyme E2 D3
formula_weight	16706.1 kDa
ec_number	2.3.2.23,2.3.2.24
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	c

MALKRINKELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDRDKYNRISREWTQKYAM

Entity 12 polymer

description	E3 ubiquitin-protein ligase UHRF1
formula_weight	88436.8 kDa
ec_number	2.3.2.27
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	d

MWIQVRTMDGKETHTVNSLSRLTKVQELRKKIEEVFHVEPQLQRLFYRGKQMEDGHTLFDYDVRLNDTIQLLVRQSLALPLSTKERDSELSDSDSGYGVGHSESDKSSTHGEGAAEADDKTVWEDTDLGLYKVNEYVDVRDNIFGAWFEAQVVQVQKRALSEDEPCSSSAVKTSEDDIMYHVKYDDYPEHGVDIVKAKNVRARARTVIPWENLEVGQVVMANYNVDYPRKRGFWYDVEICRKRQTRTARELYGNIRLLNDSQLNNCRIMFVDEVLMIELPKERRPLIASPSQPPPALRNTGKSGPSCRFCKDDENKPCRKCACHVCGGREAPEKQLLCDECDMAFHLYCLKPPLTSVPPEPEWYCPSCRTDSSEVVQAGEKLKESKKKAKMASATSSSRRDWGKGMACVGRTTECTIVPANHFGPIPGVPVGTMWRFRVQVSESGVHRPHVAGIHGRSNDGAYSLVLAGGYEDDVDNGNYFTYTGSGGRDLSGNKRTAGQSSDQKLTNNNRALALNCHSPINEKGAEAEDWRQGKPVRVVRNMKGGKHSKYAPAEGNRYDGIYKVVKYWPERGKSGFLVWRYLLRRDDTEPEPWTREGKDRTRQLGLTMQYPEGYLEALANKEKSRKRPAKALEQGPSSSKTGKSKQKSTGPTLSSPRASKKSKLEPYTLSEQQANLIKEDKGNAKLWDDVLTSLQDGPYQIFLSKVKEAFQCICCQELVFRPVTTVCQHNVCKDCLDRSFRAQVFSCPACRFELDHSSPTRVNQPLQTILNQLFPGYGSGR

Entity 13 polymer

description	Zinc finger BED domain-containing protein 3
formula_weight	25643.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	e

MKSKKPLKITMEDSRRLNDPAEQGGLCPAPVGPSYSEAWGYFHLDPAQPRHRMMSAWATCRLCGLQVGGLPNFQMWTRALCQHLSDVHLPELKKSAAPSSPTTMPCPPPPSPTMAAEGDWARLLEQMGELAMRGSQRELELERREAALMQAELELERKRQALKQEAQSVEQERHQLQVEREALSKWIKKQSPGAQVPEPPSPLPLLPKEDPDIHDNNSDNDMVTKVLL

▶

6. Citations (1)

▶

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	4.20 Å
resolution_method	—
num_particles	424595

fit	/app/data/saxs_computation/sf/9sfp/9sfp.fit
pddf	/app/data/pr_computation/sf/9sfp/9sfp.pr.out
profile	/app/data/saxs_computation/sf/9sfp/9sfp.dat

Native cytoplasmic lattices from mouse oocytes

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 (13)

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 polymer

Polymer

Entity 10 polymer

Polymer

Entity 11 polymer

Polymer

Entity 12 polymer

Polymer

Entity 13 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)