← Back to search

9ygy

Structure of a GRP94 folding intermediate engaged with a CCDC134- and FKBP11-bound secretory translocon

Method: ELECTRON MICROSCOPY D_max: 214.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9ygy
deposition_date	2025-09-29
title	Structure of a GRP94 folding intermediate engaged with a CCDC134- and FKBP11-bound secretory translocon
keywords	Ribosome, Membrane protein, Translocon, Transport, N-Glycosylation; RIBOSOME
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	64.99 Å
rg_electron	64.38 Å
i0	3511980000.00
molecular_weight	526630.0 kDa
excluded_volume	669860 Å³
envelope_volume	1122600 Å³
shell_volume	144080 Å³
envelope_diameter	283.8 Å
shell_rg	66.33 Å
envelope_rg	63.93 Å
shape_rg	64.35 Å
total_rg	64.52 Å
total_atoms	74558
n_residues	4669
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	214.7 Å
rg_real	64.79 Å
rg_real_error	1.36 Å
i0_real	3.5090e+09
i0_real_error	6.8850e+07
rg_reciprocal	65.06 Å
i0_reciprocal	3513000000.0000
total_estimate	0.8514
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	80.5 Å
skewness	0.325
kurtosis	-0.082
angular_range	— – 0.1200 Å⁻¹
current_alpha	0.0210
highest_alpha	254900000.0000
n_real_points	25
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.830; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.604

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (25)

Entity 1 polymer

description	Translocon-associated protein subunit alpha
formula_weight	32263.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	5
atom_count	74558

MRLLPRLLLLLLLVFPATVLFRGGPRGLLAVAQDLTEDEETVEDSIIEDEDDEAEVEEDEPTDLVEDKEEEDVSGEPEASPSADTTILFVKGEDFPANNIVKFLVGFTNKGTEDFIVESLDASFRYPQDYQFYIQNFTALPLNTVVPPQRQATFEYSFIPAEPMGGRPFGLVINLNYKDLNGNVFQDAVFNQTVTVIEREDGLDGETIFMYMFLAGLGLLVIVGLHQLLESRKRKRPIQKVEMGTSSQNDVDMSWIPQETLNQINKASPRRLPRKRAQKRSVGSDE

Entity 2 polymer

description	Translocon-associated protein subunit beta
formula_weight	20155.0 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	6

MRLLSFVVLALFAVTQAEEGARLLASKSLLNRYAVEGRDLTLQYNIYNVGSSAALDVELSDDSFPPEDFGIVSGMLNVKWDRIAPASNVSHTVVLRPLKAGYFNFTSATITYLAQEDGPVVIGSTSAPGQGGILAQREFDRRFSPHFLDWAAFGVMTLPSIGIPLLLWYSSKRKYDTPKTKKN

Entity 3 polymer

description	Translocon-associated protein subunit gamma
formula_weight	21106.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	7

MAPKGSSKQQSEEDLLLQDFSRNLSAKSSALFFGNAFIVSAIPIWLYWRIWHMDLIQSAVLYSVMTLVSTYLVAFAYKNVKFVLKHKVAQKREDAVSKEVTRKLSEADNRKMSRKEKDERILWKKNEVADYEATTFSIFYNNTLFLVVVIVASFFILKNFNPTVNYILSISASSGLIALLSTGSK

Entity 4 polymer

description	Translocon-associated protein subunit delta
formula_weight	19015.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	8

MAAMASLGALALLLLSSLSRCSAEACLEPQITPSYYTTSDAVISTETVFIVEISLTCKNRVQNMALYADVGGKQFPVTRGQDVGRYQVSWSLDHKSAHAGTYEVRFFDEESYSLLRKAQRNNEDISIIPPLFTVSVDHRGTWNGPWVSTEVLAAAIGLVIYYLAFSAKSHIQA

Entity 5 polymer

description	Peptidyl-prolyl cis-trans isomerase FKBP11
formula_weight	22213.4 kDa
ec_number	5.2.1.8
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

MTLRPSLLPLHLLLLLLLSAAVCRAEAGLETESPVRTLQVETLVEPPEPCAEPAAFGDTLHIHYTGSLVDGRIIDTSLTRDPLVIELGQKQVIPGLEQSLLDMCVGEKRRAIIPSHLAYGKRGFPPSVPADAVVQYDVELIALIRANYWLKLVKGILPLVGMAMVPALLGLIGYHLYRKANRPKVSKKKLKEEKRNKSKKK

Entity 6 polymer

description	Coiled-coil domain-containing protein 134
formula_weight	26598.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MDLLQFLAFLFVLLLSGMGATGTLRTSLDPSLEIYKKMFEVKRREQLLALKNLAQLNDIHQQYKILDVMLKGLFKVLEDSRTVLTAADVLPDGPFPQDEKLKDAFSHVVENTAFFGDVVLRFPRIVHYYFDHNSNWNLLIRWGISFCNQTGVFNQGPHSPILSLMAQELGISEKDSNFQNPFKIDRTEFIPSTDPFQKALREEEKRRKKEEKRKEIRKGPRISRSQSEL

Entity 7 polymer

description	Protein transport protein Sec61 subunit alpha isoform 1
formula_weight	52304.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

MAIKFLEVIKPFCVILPEIQKPERKIQFKEKVLWTAITLFIFLVCCQIPLFGIMSSDSADPFYWMRVILASNRGTLMELGISPIVTSGLIMQLLAGAKIIEVGDTPKDRALFNGAQKLFGMIITIGQSIVYVMTGMYGDPSEMGAGICLLITIQLFVAGLIVLLLDELLQKGYGLGSGISLFIATNICETIVWKAFSPTTVNTGRGMEFEGAIIALFHLLATRTDKVRALREAFYRQNLPNLMNLIATIFVFAVVIYFQGFRVDLPIKSARYRGQYNTYPIKLFYTSNIPIILQSALVSNLYVISQMLSARFSGNLLVSLLGTWSDTSSGGPARAYPVGGLCYYLSPPESFGSVLEDPVHAVVYIVFMLGSCAFFSKTWIEVSGSSAKDVAKQLKEQQMVMRGHRETSMVHELNRYIPTAAAFGGLCIGALSVLADFLGAIGSGTGILLAVTIIYQYFEIFVKEQSEVGSMGALLF

Entity 8 polymer

description	Protein transport protein Sec61 subunit beta
formula_weight	9987.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

MPGPTPSGTNVGSSGRSPSKAVAARAAGSTVRQRKNASCGTRSAGRTTSAGTGGMWRFYTEDSPGLKVGPVPVLVMSLLFIASVFMLHIWGKYTRS

Entity 9 polymer

description	Protein transport protein Sec61 subunit gamma
formula_weight	7752.3 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

MDQVMQFVEPSRQFVKDSIRLVKRCTKPDRKEFQKIAMATAIGFAIMGFIGFFVKLIHIPINNIIVGG

Entity 10 polymer

description	Stress-associated endoplasmic reticulum protein 1
formula_weight	7384.8 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

MVAKQRIRMANEKHSKNITQRGNVAKTSRNAPEEKASVGPWLLALFIFVVCGSAIFQIIQSIRMGM

Entity 11 polymer

description	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A
formula_weight	80607.3 kDa
ec_number	2.4.99.18
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

MTKFGFLRLSYEKQDTLLKLLILSMAAVLSFSTRLFAVLRFESVIHEFDPYFNYRTTRFLAEEGFYKFHNWFDDRAWYPLGRIIGGTIYPGLMITSAAIYHVLHFFHITIDIRNVCVFLAPLFSSFTTIVTYHLTKELKDAGAGLLAAAMIAVVPGYISRSVAGSYDNEGIAIFCMLLTYYMWIKAVKTGSICWAAKCALAYFYMVSSWGGYVFLINLIPLHVLVLMLTGRFSHRIYVAYCTVYCLGTILSMQISFVGFQPVLSSEHMAAFGVFGLCQIHAFVDYLRSKLNPQQFEVLFRSVISLVGFVLLTVGALLMLTGKISPWTGRFYSLLDPSYAKNNIPIIASVSEHQPTTWSSYYFDLQLLVFMFPVGLYYCFSNLSDARIFIIMYGVTSMYFSAVMVRLMLVLAPVMCILSGIGVSQVLSTYMKNLDISRPDKKSKKQQDSTYPIKNEVASGMILVMAFFLITYTFHSTWVTSEAYSSPSIVLSARGGDGSRIIFDDFREAYYWLRHNTPEDAKVMSWWDYGYQITAMANRTILVDNNTWNNTHISRVGQAMASTEEKAYEIMRELDVSYVLVIFGGLTGYSSDDINKFLWMVRIGGSTDTGKHIKENDYYTPTGEFRVDREGSPVLLNCLMYKMCYYRFGQVYTEAKRPPGFDRVRNAEIGNKDFELDVLEEAYTTEHWLVRIYKVKDLDNRGLSRT

Entity 12 polymer

description	Oligosaccharyltransferase complex subunit OSTC
formula_weight	16844.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	J

METLYRVPFLVLECPNLKLKKPPWLHMPSAMTVYALVVVSYFLITGGIIYDVIVEPPSVGSMTDEHGHQRPVAFLAYRVNGQYIMEGLASSFLFTMGGLGFIILDRSNAPNIPKLNRFLLLFIGFVCVLLSFFMARVFMRMKLPGYLMG

Entity 13 polymer

description	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4
formula_weight	4196.0 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	K2

MITDVQLAIFANMLGVSLFLLVVLYHYVAVNNPKKQE

Entity 14 polymer

description	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit TMEM258
formula_weight	9083.8 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L2

MELEAMSRYTSPVNPAVFPHLTVVLLAIGMFFTAWFFVYEVTSTKYTRDIYKELLISLVASLFMGFGVLFLLLWVGIYV

Entity 15 polymer

description	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1
formula_weight	12503.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	M2

MSASVVSVISRFLEEYLSSTPQRLKLLDAYLLYILLTGALQFGYCLLVGTFPFNSFLSGFISCVGSFILAVCLRIQINPQNKADFQGISPERAFADFLFASTILHLVVMNFVG

Entity 16 polymer

description	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit KCP2
formula_weight	14689.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	N

MVVGTGTSLALSSLLSLLLFAGMQMYSRQLASTEWLTIQGGLLGSGLFVFSLTAFNNLENLVFGKGFQAKIFPEILLCLLLALFASGLIHRVCVTTCFIFSMVGLYYINKISSTLYQAAAPVLTPAKVTGKSKKRN

Entity 17 polymer

description	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit
formula_weight	50854.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	N2

MGYFRCARAGSFGRRRKMEPSTAARAWALFWLLLPLLGAVCASGPRTLVLLDNLNVRETHSLFFRSLKDRGFELTFKTADDPSLSLIKYGEFLYDNLIIFSPSVEDFGGNINVETISAFIDGGGSVLVAASSDIGDPLRELGSECGIEFDEEKTAVIDHHNYDISDLGQHTLIVADTENLLKAPTIVGKSSLNPILFRGVGMVADPDNPLVLDILTGSSTSYSFFPDKPITQYPHAVGKNTLLIAGLQARNNARVIFSGSLDFFSDSFFNSAVQKAAPGSQRYSQTGNYELAVALSRWVFKEEGVLRVGPVSHHRVGETAPPNAYTVTDLVEYSIVIQQLSNGKWVPFDGDDIQLEFVRIDPFVRTFLKKKGGKYSVQFKLPDVYGVFQFKVDYNRLGYTHLYSSTQVSVRPLQHTQYERFIPSAYPYYASAFSMMLGLFIFSIVFLHMKEKEKSD

Entity 18 polymer

description	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1
formula_weight	68656.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	O2

MEAPAAGLFLLLLLGTWAPAPGSASSEAPPLINEDVKRTVDLSSHLAKVTAEVVLAHLGGGSTSRATSFLLALEPELEARLAHLGVQVKGEDEEENNLEVRETKIKGKSGRFFTVKLPVALDPGAKISVIVETVYTHVLHPYPTQITQSEKQFVVFEGNHYFYSPYPTKTQTMRVKLASRNVESYTKLGNPTRSEDLLDYGPFRDVPAYSQDTFKVHYENNSPFLTITSMTRVIEVSHWGNIAVEENVDLKHTGAVLKGPFSRYDYQRQPDSGISSIRSFKTILPAAAQDVYYRDEIGNVSTSHLLILDDSVEMEIRPRFPLFGGWKTHYIVGYNLPSYEYLYNLGDQYALKMRFVDHVFDEQVIDSLTVKIILPEGAKNIEIDSPYEISRAPDELHYTYLDTFGRPVIVAYKKNLVEQHIQDIVVHYTFNKVLMLQEPLLVVAAFYILFFTVIIYVRLDFSITKDPAAEARMKVACITEQVLTLVNKRIGLYRHFDETVNRYKQSRDISTLNSGKKSLETEHKALTSEIALLQSRLKTEGSDLCDRVSEMQKLDAQVKELVLKSAVEAERLVAGKLKKDTYIENEKLISGKRQELVTKIDHILDAL

Entity 19 polymer

description	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2
formula_weight	69347.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	P2

MAPPGSSTVFLLALTIIASTWALTPTHYLTKHDVERLKASLDRPFTNLESAFYSIVGLSSLGAQVPDAKKACTYIRSNLDPSNVDSLFYAAQASQALSGCEISISNETKDLLLAAVSEDSSVTQIYHAVAALSGFGLPLASQEALSALTARLSKEETVLATVQALQTASHLSQQADLRSIVEEIEDLVARLDELGGVYLQFEEGLETTALFVAATYKLMDHVGTEPSIKEDQVIQLMNAIFSKKNFESLSEAFSVASAAAVLSHNRYHVPVVVVPEGSASDTHEQAILRLQVTNVLSQPLTQATVKLEHAKSVASRATVLQKTSFTPVGDVFELNFMNVKFSSGYYDFLVEVEGDNRYIANTVELRVKISTEVGITNVDLSTVDKDQSIAPKTTRVTYPAKAKGTFIADSHQNFALFFQLVDVNTGAELTPHQTFVRLHNQKTGQEVVFVAEPDNKNVYKFELDTSERKIEFDSASGTYTLYLIIGDATLKNPILWNVADVVIKFPEEEAPSTVLSQNLFTPKQEIQHLFREPEKRPPTVVSNTFTALILSPLLLLFALWIRIGANVSNFTFAPSTIIFHLGHAAMLGLMYVYWTQLNMFQTLKYLAILGSVTFLAGNRMLAQQAVKRTAH

Entity 20 polymer

description	Endoplasmin
formula_weight	96254.2 kDa
ec_number	3.6.4.-
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	y3

MRALWVLGLCCVLLTFGSVRADDEVDVDGTVEEDLGKSREGSRTDDEVVQREEEAIQLDGLNASQIRELREKSEKFAFQAEVNRMMKLIINSLYKNKEIFLRELISNASDALDKIRLISLTDENALSGNEELTVKIKCDKEKNLLHVTDTGVGMTREELVKNLGTIAKSGTSEFLNKMTEAQEDGQSTSELIGQFGVGFYSAFLVADKVIVTSKHNNDTQHIWESDSNEFSVIADPRGNTLGRGTTITLVLKEEASDYLELDTIKNLVKKYSQFINFPIYVWSSKTETVEEPMEEEEAAKEEKEESDDEAAVEEEEEEKKPKTKKVEKTVWDWELMNDIKPIWQRPSKEVEEDEYKAFYKSFSKESDDPMAYIHFTAEGEVTFKSILFVPTSAPRGLFDEYGSKKSDYIKLYVRRVFITDDFHDMMPKYLNFVKGVVDSDDLPLNVSRETLQQHKLLKVIRKKLVRKTLDMIKKIADDKYNDTFWKEFGTNIKLGVIEDHSNRTRLAKLLRFQSSHHPTDITSLDQYVERMKEKQDKIYFMAGSSRKEAESSPFVERLLKKGYEVIYLTEPVDEYCIQALPEFDGKRFQNVAKEGVKFDESEKTKESREAVEKEFEPLLNWMKDKALKDKIEKAVVSQRLTESPCALVASQYGWSGNMERIMKAQAYQTGKDISTNYYASQKKTFEINPRHPLIRDMLRRIKEDEDDKTVLDLAVVLFETATLRSGYLLPDTKAYGDRIERMLRLSLNIDPDAKVEEEPEEEPEETAEDTTEDTEQDEDEEMDVGTDEEEETAKESTAEKDELXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Entity 21 branched

description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[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	1397.2 kDa
src_method	man
entity_count	1

Entity 22 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	1

Entity 23 branched

description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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	1397.2 kDa
src_method	man
entity_count	1

Entity 24 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	1

Entity 25 non-polymer

description	phosphono [(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl] hydrogen phosphate
formula_weight	452.5 kDa
src_method	syn
entity_count	1

▶

6. Citations (2)

▶

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	4.10 Å
resolution_method	—
num_particles	55750

fit	/app/data/saxs_computation/yg/9ygy/9ygy.fit
pddf	/app/data/pr_computation/yg/9ygy/9ygy.pr.out
profile	/app/data/saxs_computation/yg/9ygy/9ygy.dat

Structure of a GRP94 folding intermediate engaged with a CCDC134- and FKBP11-bound secretory translocon

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 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

Entity 14 polymer

Polymer

Entity 15 polymer

Polymer

Entity 16 polymer

Polymer

Entity 17 polymer

Polymer

Entity 18 polymer

Polymer

Entity 19 polymer

Polymer

Entity 20 polymer

Polymer

Entity 21 branched

Entity 22 branched

Entity 23 branched

Entity 24 branched

Entity 25 non-polymer

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)