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9uh9

human Ribonuclease MRP state 1

Method: ELECTRON MICROSCOPY D_max: 180.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uh9
deposition_date	2025-04-14
title	human Ribonuclease MRP state 1
keywords	RNase MRP, RNA BINDING PROTEIN/RNA, RNA BINDING PROTEIN-RNA complex; RNA BINDING PROTEIN/RNA
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	53.22 Å
rg_electron	53.97 Å
i0	2811190000.00
molecular_weight	390860.0 kDa
excluded_volume	467470 Å³
envelope_volume	731280 Å³
shell_volume	111570 Å³
envelope_diameter	190.6 Å
shell_rg	58.27 Å
envelope_rg	53.16 Å
shape_rg	53.99 Å
total_rg	54.03 Å
total_atoms	27111
n_residues	2995
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	180.2 Å
rg_real	53.21 Å
rg_real_error	1.45 Å
i0_real	2.8110e+09
i0_real_error	5.0880e+07
rg_reciprocal	53.23 Å
i0_reciprocal	2811000000.0000
total_estimate	0.8681
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	60.0 Å
skewness	0.359
kurtosis	-0.266
angular_range	— – 0.1500 Å⁻¹
current_alpha	0.0000
highest_alpha	245600000.0000
n_real_points	31
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.836; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.789

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4. Crystallography & Experiment

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5. Entities & Polymer Info (13)

Entity 1 polymer

description	RNA (270-MER)
formula_weight	86578.1 kDa
src_method	nat
entity_count	1

Polymer

type	polyribonucleotide
strand_id	A
atom_count	27111

UGGUUCGUGCUGAAGGCCUGUAUCCUAGGCUACACACUGAGGACUCUGUUCCUCCCCUUUCCGCCUAGGGGAAAGUCCCCGGACCUCGGGCAGAGAGUGCCACGUGCAUACGCACGUAGACAUUCCCCGCUUCCCACUCCAAAGUCCGCCAAGAAGCGUAUCCCGCUGAGCGGCGUGGCGCGGGGGCGUCAUCCGUCAGCUCCCUCUAGUUACGCAGGCAGUGCGUGUCCGCGCACCAACCACACGGGGCUCAUUCUCAGCGCGGCUGUU

Entity 2 polymer

description	Ribonucleases P/MRP protein subunit POP1
formula_weight	114896.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MSNAKERKHAKKMRNQPTNVTLSSGFVADRGVKHHSGGEKPFQAQKQEPHPGTSRQRQTRVNPHSLPDPEVNEQSSSKGMFRKKGGWKAGPEGTSQEIPKYITASTFAQARAAEISAMLKAVTQKSSNSLVFQTLPRHMRRRAMSHNVKRLPRRLQEIAQKEAEKAVHQKKEHSKNKCHKARRCHMNRTLEFNRRQKKNIWLETHIWHAKRFHMVKKWGYCLGERPTVKSHRACYRAMTNRCLLQDLSYYCCLELKGKEEEILKALSGMCNIDTGLTFAAVHCLSGKRQGSLVLYRVNKYPREMLGPVTFIWKSQRTPGDPSESRQLWIWLHPTLKQDILEEIKAACQCVEPIKSAVCIADPLPTPSQEKSQTELPDEKIGKKRKRKDDGENAKPIKKIIGDGTRDPCLPYSWISPTTGIIISDLTMEMNRFRLIGPLSHSILTEAIKAASVHTVGEDTEETPHRWWIETCKKPDSVSLHCRQEAIFELLGGITSPAEIPAGTILGLTVGDPRINLPQKKSKALPNPEKCQDNEKVRQLLLEGVPVECTHSFIWNQDICKSVTENKISDQDLNRMRSELLVPGSQLILGPHESKIPILLIQQPGKVTGEDRLGWGSGWDVLLPKGWGMAFWIPFIYRGVRVGGLKESAVHSQYKRSPNVPGDFPDCPAGMLFAEEQAKNLLEKYKRRPPAKRPNYVKLGTLAPFCCPWEQLTQDWESRVQAYEEPSVASSPNGKESDLRRSEVPCAPMPKKTHQPSDEVGTSIEHPREAEEVMDAGCQESAGPERITDQEASENHVAATGSHLCVLRSRKLLKQLSAWCGPSSEDSRGGRRAPGRGQQGLTREACLSILGHFPRALVWVSLSLLSKGSPEPHTMICVPAKEDFLQLHEDWHYCGPQESKHSDPFRSKILKQKEKKKREKRQKPGRASSDGPAGEEPVAGQEALTLGLWSGPLPRVTLHCSRTLLGFVTQGDFSMAVGCGEALGFVSLTGLLDMLSSQPAAQRGLVLLRPPASLQYRFARIAIEV

Entity 3 polymer

description	Ribonuclease P protein subunit p38
formula_weight	31891.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MAAAPQAPGRGSLRKTRPLVVKTSLNNPYIIRWSALESEDMHFILQTLEDRLKAIGLQKIEDKKKKNKTPFLKKESREKCSIAVDISENLKEKKTDAKQQVSGWTPAHVRKQLAIGVNEVTRALERRELLLVLVCKSVKPAMITSHLIQLSLSRSVPACQVPRLSERIAPVIGLKCVLALAFKKNTTDFVDEVRAIIPRVPSLSVPWLQDRIEDSGENLETEPLESQDRELLDTSFEDLSKPKRKLADGRQASVTLQPLKIKKLIPNPNKIRKPPKSKKATPK

Entity 4 polymer

description	Ribonuclease P protein subunit p29
formula_weight	25474.9 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

MKSVIYHALSQKEANDSDVQPSGAQRAEAFVRAFLKRSTPRMSPQAREDQLQRKAVVLEYFTRHKRKEKKKKAKGLSARQRRELRLFDIKPEQQRYSLFLPLHELWKQYIRDLCSGLKPDTQPQMIQAKLLKADLHGAIISVTKSKCPSYVGITGILLQETKHIFKIITKEDRLKVIPKLNCVFTVETDGFISYIYGSKFQLRSSERSAKKFKAKGTIDL

Entity 5 polymer

description	Ribonuclease P/MRP protein subunit POP5
formula_weight	18844.7 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

MVRFKHRYLLCELVSDDPRCRLSLDDRVLSSLVRDTIARVHGTFGAAACSIGFAVRYLNAYTGIVLLRCRKEFYQLVWSALPFITYLENKGHRYPCFFNTLHVGGTIRTCQKFLIQYNRRQLLILLQNCTDEGEREAIQKSVTRSCLLEEEEESGEEAAEAME

Entity 6 polymer

description	Ribonuclease P protein subunit p25
formula_weight	20659.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

MENFRKVRSEEAPAGCGAEGGGPGSGPFADLAPGAVHMRVKEGSKIRNLMAFATASMAQPATRAIVFSGCGRATTKTVTCAEILKRRLAGLHQVTRLRYRSVREVWQSLPPGPTQGQTPGEPAASLSVLKNVPGLAILLSKDALDPRQPGYQPPNPHPGPSSPPAAPASKRSLGEPAAGEGSAKRSQPEPGVADEDQTA

Entity 7 polymer

description	Ribonuclease P protein subunit p20
formula_weight	15672.9 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

MAENREPRGAVEAELDPVEYTLRKRLPSRLPRRPNDIYVNMKTDFKAQLARCQKLLDGGARGQNACSEIYIHGLGLAINRAINIALQLQAGSFGSLQVAANTSTVELVDELEPETDTREPLTRIRNNSAIHIRVFRVTPK

Entity 8 polymer

description	Ribonuclease P protein subunit p14
formula_weight	13707.0 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

MPAPAATYERVVYKNPSEYHYMKVCLEFQDCGVGLNAAQFKQLLISAVKDLFGEVDAALPLDILTYEEKTLSAILRICSSGLVKLWSSLTLLGSYKGKKCAFRVIQVSPFLLALSGNSRELVLD

Entity 9 polymer

description	Ribonuclease P protein subunit p30
formula_weight	29364.3 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	I,J

MAVFADLDLRAGSDLKALRGLVETAAHLGYSVVAINHIVDFKEKKQEIEKPVAVSELFTTLPIVQGKSRPIKILTRLTIIVSDPSHCNVLRATSSRARLYDVVAVFPKTEKLFHIACTHLDVDLVCITVTEKLPFYFKRPPINVAIDRGLAFELVYSPAIKDSTMRRYTISSALNLMQICKGKNVIISSAAERPLEIRGPYDVANLGLLFGLSESDAKAAVSTNCRAALLHGETRKTAFGIISTVKKPRPSEGDEDCLPASKKAKCEG

Entity 10 polymer

description	UPF0711 protein C18orf21
formula_weight	24876.9 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	K

MRQKHYLEAAARGLHDSCPGQARYLLWAYTSSHDDKSTFEETCPYCFQLLVLDNSRVRLKPKARLTPKIQKLLNREARNYTLSFKEAKMVKKFKDSKSVLLITCKTCNRTVKHHGKSRSFVSTLKSNPATPTSKLSLKTPERRTANPNHDMSGSKGKSPASVFRTPTSGQSVSTCSSKNTSKTKKHFSQLKMLLSQNESQKIPKVDFRNFLSSLKGGLLK

Entity 11 polymer

description	Ribonuclease P protein subunit p40
formula_weight	41884.8 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

MATLRRLREAPRHLLVCEKSNFGNHKSRHRHLVQTHYYNYRVSFLIPECGILSEELKNLVMNTGPYYFVKNLPLHELITPEFISTFIKKGSCYALTYNTHIDEDNTVALLPNGKLILSLDKDTYEETGLQGHPSQFSGRKIMKFIVSIDLMELSLNLDSKKYERISWSFKEKKPLKFDFLLAWHKTGSEESTMMSYFSKYQIQEHQPKVALSTLRDLQCPVLQSSELEGTPEVSCRALELFDWLGAVFSNVDLNNEPNNFISTYCCPEPSTVVAKAYLCTITGFILPEKICLLLEHLCHYFDEPKLAPWVTLSVQGFADSPVSWEKNEHGFRKGGEHLYNFVIFNNQDYWLQMAVGANDHCPP

Entity 12 polymer

description	Nucleolus and neural progenitor protein
formula_weight	64653.8 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	M

MMAAVPPGLEPWNRVRIPKAGNRSAVTVQNPGAALDLCIAAVIKECHLVILSLKSQTLDAETDVLCAVLYSNHNRMGRHKPHLALKQVEQCLKRLKNMNLEGSIQDLFELFSSNENQPLTTKVCVVPSQPVVELVLMKVLGACKLLLRLLDCCCKTFLLTVKHLGLQEFIILNLVMVGLVSRLWVLYKGVLKRLILLYEPLFGLLQEVARIQPMPYFKDFTFPSDITEFLGQPYFEAFKKKMPIAFAAKGINKLLNKLFLINEQSPRASEETLLGISKKAKQMKINVQNNVDLGQPVKNKRVFKEESSEFDVRAFCNQLKHKATQETSFDFKCSQSRLKTTKYSSQKVIGTPHAKSFVQRFREAESFTQLSEEIQMAVVWCRSKKLKAQAIFLGNKLLKSNRLKHLEAQGTSLPKKLECIKTSICNHLLRGSGIKTSKHHLRQRRSQNKFLRRQRKPQRKLQSTLLREIQQFSQGTRKSATDTSAKWRLSHCTVHRTDLYPNSKQLLNSGVSMPVIQTKEKMIHENLRGIHENETDSWTVMQINKNSTSGTIKETDDIDDIFALMGV

Entity 13 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

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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	—

resolution	3.470 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.47 Å
resolution_method	—
num_particles	432377

fit	/app/data/saxs_computation/uh/9uh9/9uh9.fit
pddf	/app/data/pr_computation/uh/9uh9/9uh9.pr.out
profile	/app/data/saxs_computation/uh/9uh9/9uh9.dat

human Ribonuclease MRP state 1

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

Refinement

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 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)