SAXSdb — 9cok

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Phosphoprotein

Henipavirus nipahense

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	RNA-directed RNA polymerase L × 1 （Q997F0）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PHOSP_NIPAV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 51–759； UniProt 1–709 Author chain C； PDBConstruct 51–759； UniProt 1–709 Author chain D； PDBConstruct 51–759； UniProt 1–709 Author chain E； PDBConstruct 51–759； UniProt 1–709 Author chain F； PDBConstruct 51–759； UniProt 1–709 Author chain G； PDBConstruct 51–759； UniProt 1–709

RNA-directed RNA polymerase L

Henipavirus nipahense

UniProt Q997F0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Phosphoprotein × 6 （Q9IK91）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	L_NIPAV
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 27–2270； UniProt 1–2244

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9cok
Deposition date deposition_date	2024-07-16
Structure title title	Cryo-EM structure of the Nipah virus (Malaysia Strain) L:P complex
Keywords keywords	RNA dependent RNA polymerase, Nipah virus, LP complex, VIRAL PROTEIN, TRANSFERASE; VIRAL PROTEIN, TRANSFERASE
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9cok__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9cok__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9cok__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	39.46 Å
Rg (electron density)	39.29 Å
Total Rg	39.68 Å
Atom count	12206
Residues	1524
Excluded volume	219110 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9cok__assembly_1__model_1`	heptameric （7）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Phosphoprotein
Molecular weight formula_weight	84026.4 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,C,E,F,G
Atom count atom_count	12206

MKSSWSHPQFEKGAMTGWSHPQFEKGSSASWSHPQFEKGAENLYFQSNGSMDKLELVNDGLNIIDFIQKNQKEIQKTYGRSSIQQPSIKDQTKAWEDFLQCTSGESEQVEGGMSKDDGDVERRNLEDLSSTSPTDGTIGKRVSNTRDWAEGSDDIQLDPVVTDVVYHDHGGECTGYGFTSSPERGWSDYTSGANNGNVCLVSDAKMLSYAPEIAVSKEDRETDLVHLENKLSTTGLNPTAVPFTLRNLSDPAKDSPVIAEHYYGLGVKEQNVGPQTSRNVNLDSIKLYTSDDEEADQLEFEDEFAGSSSEVIVGISPEDEEPSSVGGKPNESIGRTIEGQSIRDNLQAKDNKSTDVPGAGPKDSAVKEEPPQKRLPMLAEEFECSGSEDPIIRELLKENSLINCQQGKDAQPPYHWSIERSISPDKTEIVNGAVQTADRQRPGTPMPKSRGIPIKKGTDAKYPSAGTENVPGSKSGATRHVRGSPPYQEGKSVNAENVQLNASTAVKETDKSEVNPVDDNDSLDDKYIMPSDDFSNTFFPHDTDRLNYHADHLGDYDLETLCEESVLMGVINSIKLINLDMRLNHIEEQVKEIPKIINKLESIDRVLAKTNTALSTIEGHLVSMMIMIPGKGKGERKGKNNPELKPVIGRDILEQQSLFSFDNVKNFRDGSLTNEPYGAAVQLREDLILPELNFEETNASQFVPMADDSSRDVIKTLIRTHIKDRELRSELIGYLNKAENDEEIQEIANTVNDIIDGNI

Source Source

Source organism organism	Henipavirus nipahense
NCBI taxonomy ID ncbi_taxonomy_id	3052225
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	RNA-directed RNA polymerase L
Molecular weight formula_weight	260638.6 kDa
EC 编号 ec_number	2.7.7.48,3.6.1.-,2.7.7.88,2.1.1.375
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MKSSHHHHHHHHHHGSSENLYFQSGSMADELSISDIIYPECHLDSPIVSGKLISAIEYAQLRHNQPSDDKRLSENIRLNLHGKRKSLYILRQSKQGDYIRNNIKNLKEFMHIAYPECNNILFSITSQGMTSKLDNIMKKSFKAYNIISKKVIGMLQNITRNLITQDRRDEIINIHECRRLGDLGKNMSQSKWYECFLFWFTIKTEMRAVIKNSQKPKFRSDSCIIHMRDKSTEIILNPNLICIFKSDKTGKKCYYLTPEMVLMYCDVLEGRMMMETTVKSDIKYQPLISRSNALWGLIDPLFPVMGNRIYNIVSMIEPLVLALLQLKDEARILRGAFLHHCIKEMHQELSECGFTDQKIRSMFIDDLLSILNIDNIHLLAEFFSFFRTFGHPILEAKVAAEKVREHMLADKVLEYAPIMKAHAIFCGTIINGYRDRHGGAWPPLYLPAHASKHIIRLKNSGESLTIDDCVKNWESFCGIQFDCFMELKLDSDLSMYMKDKALSPIKDEWDSVYPREVLSYTPPKSTEPRRLVDVFVNDENFDPYNMLEYVLSGAYLEDEQFNVSYSLKEKETKQAGRLFAKMTYKMRACQVIAEALIASGVGKYFKENGMVKDEHELLKTLFQLSISSVPRGNSQGNDPQSINNIERDFQYFKGVTTNVKDKKNNSFNKVKSALNNPCQADGVHHNMSPNTRNRYKCSNTSKSFLDYHTEFNPHNHYKSDNTEAAVLSRYEDNTGTKFDTVSAFLTTDLKKFCLNWRYESMAIFAERLDEIYGLPGFFNWMHKRLERSVIYVADPNCPPNIDKHMELEKTPEDDIFIHYPKGGIEGYSQKTWTIATIPFLFLSAYETNTRIAAIVQGDNESIAITQKVHPNLPYKVKKEICAKQAQLYFERLRMNLRALGHNLKATETIISTHLFIYSKKIHYDGAVLSQALKSMSRCCFWSETLVDETRSACSNISTTIAKAIENGLSRNVGYCINILKVIQQLLISTEFSINETLTLDVTSPISNNLDWLITAALIPAPIGGFNYLNLSRIFVRNIGDPVTASLADLKRMIDHSIMTESVLQKVMNQEPGDASFLDWASDPYSGNLPDSQSITKTIKNITARTILRNSPNPMLKGLFHDKSFDEDLELASFLMDRRVILPRAAHEILDNSLTGAREEIAGLLDTTKGLIRSGLRKSGLQPKLVSRLSHHDYNQFLILNKLLSNRRQNDLISSNTCSVDLARALRSHMWRELALGRVIYGLEVPDALEAMVGRYITGSLECQICEQGNTMYGWFFVPRDSQLDQVDREHSSIRVPYVGSSTDERSDIKLGNVKRPTKALRSAIRIATVYTWAYGDNEECWYEAWYLASQRVNIDLDVLKAITPVSTSNNLSHRLRDKSTQFKFAGSVLNRVSRYVNISNDNLDFRIEGEKVDTNLIYQQAMLLGLSVLEGKFRLRLETDDYNGIYHLHVKDNCCVKEVADVGQVDAELPIPEYTEVDNNHLIYDPDPVSEIDCSRLSNQESKSRELDFPLWSTEELHDVLAKTVAQTVLEIITKADKDVLKQHLAIDSDDNINSLITEFLIVDPELFALYLGQSISIKWAFEIHHRRPRGRHTMVDLLSDLVSNTSKHTYKVLSNALSHPRVFKRFVNCGLLLPTQGPYLHQQDFEKLSQNLLVTSYMIYLMNWCDFKKSPFLIAEQDETVISLREDIITSKHLCVIIDLYANHHKPPWIIDLNPQEKICVLRDFISKSRHVDTSSRSWNTSDLDFVIFYASLTYLRRGIIKQLRIRQVTEVIDTTTMLRDNIIVENPPIKTGVLDIRGCIIYNLEEILSMNTKSASKKIFNLNSRPSVENHKYRRIGLNSSSCYKALNLSPLIQRYLPSGAQRLFIGEGSGSMMLLYQSTLGQSISFYNSGIDGDYIPGQRELKLFPSEYSIAEEDPSLTGKLKGLVVPLFNGRPETTWIGNLDSYEYIINRTAGRSIGLVHSDMESGIDKNVEEILVEHSHLISIAINVMMEDGLLVSKIAYTPGFPISRLFNMYRSYFGLVLVCFPVYSNPDSTEVYLLCLQKTVKTIVPPQKVLEHSNLHDEVNDQGITSVIFKIKNSQSKQFHDDLKKYYQIDQPFFVPTKITSDEQVLLQAGLKLNGPEILKSEISYDIGSDINTLRDTIIIMLNEAMNYFDDNRSPSHHLEPYPVLERTRIKTIMNCVTKKVIVYSLIKFKDTKSSELYHIKNNIRRKVLILDFRSKLMTKTLPKGMQERREKNGFKEVWIVDLSNREVKIWWKIIGYISII

Source Source

Source organism organism	Henipavirus nipahense
NCBI taxonomy ID ncbi_taxonomy_id	3052225
Host organism host_organism	Spodoptera frugiperda

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	2.92 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	258905

Cryo-EM structure of the Nipah virus (Malaysia Strain) L:P complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

Phosphoprotein

State in the Current Structure

Other States of the Same Protein in the Database

RNA-directed RNA polymerase L

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9cok__assembly_1__model_1

9cok__assembly_1__model_1 | I(q)

9cok__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

7. Citations (1)

Cryo-EM structure of the Nipah virus (Malaysia Strain) L:P complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

Phosphoprotein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

RNA-directed RNA polymerase L

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9cok__assembly_1__model_1

9cok__assembly_1__model_1 | I(q)

9cok__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

7. Citations (1)