[English] 日本語

Yorodumi

- PDB-7ltu: AALALL SEGMENT FROM THE NUCLEOPROTEIN OF SARS-COV-2, RESIDUES 217... -

+
Open data

-
Basic information

Entry

Database: PDB / ID: 7ltu

Title

AALALL SEGMENT FROM THE NUCLEOPROTEIN OF SARS-COV-2, RESIDUES 217-222, CRYSTAL FORM 1

Components

AALALL SEGMENT FROM THE NUCLEOPROTEIN OF SARS-COV-2,RESIDUES 217-222

Keywords

PROTEIN FIBRIL / amyloid fibril

Function / homology

trifluoroacetic acid

Function and homology information

Biological species

SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS 2

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.122 Å

Model details

Amyloid Fibril

Authors

Zee, C.-T. / Sawaya, M.R. / Rodriguez, J.A. / Eisenberg, D.S.

Funding support

United States, 1items

Citation

Journal: Biorxiv / Year: 2021
Title: Inhibition of amyloid formation of the Nucleoprotein of SARS-CoV-2.
Authors: Tayeb-Fligelman, E. / Cheng, X. / Tai, C. / Bowler, J.T. / Griner, S. / Sawaya, M.R. / Seidler, P.M. / Jiang, Y.X. / Lu, J. / Rosenberg, G.M. / Salwinski, L. / Abskharon, R. / Zee, C.T. / ...

History

Deposition	Feb 20, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 17, 2021	Provider: repository / Type: Initial release
Revision 1.1	Mar 24, 2021	Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Mar 6, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

-
Downloads & links

-
Download

PDBx/mmCIF format	7ltu.cif.gz	19.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7ltu.ent.gz	11.6 KB	Display	PDB format
PDBx/mmJSON format	7ltu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7ltu_validation.pdf.gz	416.6 KB	Display	wwPDB validaton report
Full document	7ltu_full_validation.pdf.gz	416.5 KB	Display
Data in XML	7ltu_validation.xml.gz	2.7 KB	Display
Data in CIF	7ltu_validation.cif.gz	2.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lt/7ltu ftp://data.pdbj.org/pub/pdb/validation_reports/lt/7ltu	HTTPS FTP

-
Related structure data

Related structure data	7luxC 7luzC 7lv2C C: citing same article (ref.)
Similar structure data	1txb-d 1ata-d 2ckx-d 4onk-1 3gcc-d 1nvl-d 1atd-d 1cir-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#189 - Sep 2015 Amyloids similarity (1)

-
Assembly

Deposited unit

A: AALALL SEGMENT FROM THE NUCLEOPROTEIN OF SARS-COV-2,RESIDUES 217-222

B: AALALL SEGMENT FROM THE NUCLEOPROTEIN OF SARS-COV-2,RESIDUES 217-222

hetero molecules

1.48 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: AALALL SEGMENT FROM THE NUCLEOPROTEIN OF SARS-COV-2,RESIDUES 217-222

B: AALALL SEGMENT FROM THE NUCLEOPROTEIN OF SARS-COV-2,RESIDUES 217-222

hetero molecules

A: AALALL SEGMENT FROM THE NUCLEOPROTEIN OF SARS-COV-2,RESIDUES 217-222

B: AALALL SEGMENT FROM THE NUCLEOPROTEIN OF SARS-COV-2,RESIDUES 217-222

hetero molecules

A: AALALL SEGMENT FROM THE NUCLEOPROTEIN OF SARS-COV-2,RESIDUES 217-222

B: AALALL SEGMENT FROM THE NUCLEOPROTEIN OF SARS-COV-2,RESIDUES 217-222

hetero molecules

A: AALALL SEGMENT FROM THE NUCLEOPROTEIN OF SARS-COV-2,RESIDUES 217-222

B: AALALL SEGMENT FROM THE NUCLEOPROTEIN OF SARS-COV-2,RESIDUES 217-222

hetero molecules

A: AALALL SEGMENT FROM THE NUCLEOPROTEIN OF SARS-COV-2,RESIDUES 217-222

B: AALALL SEGMENT FROM THE NUCLEOPROTEIN OF SARS-COV-2,RESIDUES 217-222

hetero molecules

A: AALALL SEGMENT FROM THE NUCLEOPROTEIN OF SARS-COV-2,RESIDUES 217-222

B: AALALL SEGMENT FROM THE NUCLEOPROTEIN OF SARS-COV-2,RESIDUES 217-222

hetero molecules

defined by author
8.9 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	1_455	x-1,y,z	1
crystal symmetry operation	1_655	x+1,y,z	1
crystal symmetry operation	1_565	x,y+1,z	1
crystal symmetry operation	1_465	x-1,y+1,z	1
crystal symmetry operation	1_665	x+1,y+1,z	1

Unit cell

Length a, b, c (Å)	9.450, 11.340, 20.270
Angle α, β, γ (deg.)	74.880, 79.130, 67.770
Int Tables number	1
Space group name H-M	P1

-
Components

#1: Protein/peptide	AALALL SEGMENT FROM THE NUCLEOPROTEIN OF SARS-COV-2,RESIDUES 217-222 Mass: 570.722 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS 2
#2: Chemical	ChemComp-TFA / trifluoroacetic acid Mass: 114.023 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂HF₃O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experimental details

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 1.69 Å³/Da / Density % sol: 27.3 %
Crystal grow	Temperature: 298 K / Method: batch mode / pH: 4 / Details: trifluoroacetic acid

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-E / Wavelength: 0.9792 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2020

Radiation

Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9792 Å / Relative weight: 1

Reflection

Resolution: 1.12→19.47 Å / Num. obs: 2270 / % possible obs: 78.4 % / Redundancy: 2.366 % / B_iso Wilson estimate: 14.896 Å² / CC_1/2: 0.985 / R_merge(I) obs: 0.084 / R_rim(I) all: 0.107 / Χ²: 0.879 / Net I/σ(I): 5.92

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.12-1.18	2.375	0.397	2.02	136	0.892	0.511	31.1
1.18-1.25	2.359	0.27	2.95	287	0.924	0.347	74.4
1.25-1.34	2.42	0.199	3.53	324	0.98	0.254	84.2
1.34-1.45	2.41	0.215	4.14	310	0.956	0.272	85.2
1.45-1.59	2.403	0.154	5.77	293	0.967	0.196	91
1.59-1.77	2.381	0.125	6.83	244	0.964	0.159	91.4
1.77-2.05	2.336	0.082	8.2	229	0.991	0.105	89.5
2.05-2.51	2.322	0.077	9.91	205	0.99	0.099	93.2
2.51-3.55	2.197	0.074	10.54	157	0.994	0.096	93.5
3.55-19.47	2.341	0.074	11.51	85	0.982	0.094	95.5

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	1.12 Å	19.47 Å
Translation	1.12 Å	19.47 Å

-
Processing

Software

Name	Version	Classification	NB
XDS		data reduction
XSCALE		data scaling
PHASER	2.8.3	phasing
REFMAC	5.8.0267	refinement
PDB_EXTRACT	3.27	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: ideal beta strand, AAAAAA

Resolution: 1.122→19.469 Å / Cor.coef. F_o:F_c: 0.981 / Cor.coef. F_o:F_c free: 0.964 / SU B: 2.435 / SU ML: 0.045 / Cross valid method: FREE R-VALUE / ESU R: 0.059 / ESU R Free: 0.055
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1953	227	10.004 %
R_work	0.1548	2042	-
all	0.159	-	-
obs	-	2269	79.114 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 12.753 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.438 Å²	-0.528 Å²	-0.809 Å²
2-	-	0.262 Å²	1.611 Å²
3-	-	-	0.12 Å²

Refinement step

Cycle: LAST / Resolution: 1.122→19.469 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	80	0	21	1	102

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.015	96
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	100
X-RAY DIFFRACTION	r_angle_refined_deg	1.306	1.614	133
X-RAY DIFFRACTION	r_angle_other_deg	1.311	1.607	224
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.953	5	10
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.602	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	12
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	98
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	10
X-RAY DIFFRACTION	r_nbd_refined	0.136	0.2	6
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.172	0.2	56
X-RAY DIFFRACTION	r_nbtor_refined	0.131	0.2	31
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.105	0.2	50
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.068	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.206	0.2	9
X-RAY DIFFRACTION	r_nbd_other	0.208	0.2	8
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.09	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	1.731	1.022	46
X-RAY DIFFRACTION	r_mcbond_other	1.671	1.012	45
X-RAY DIFFRACTION	r_mcangle_it	1.955	1.534	54
X-RAY DIFFRACTION	r_mcangle_other	1.978	1.539	55
X-RAY DIFFRACTION	r_scbond_it	3.925	1.562	50
X-RAY DIFFRACTION	r_scbond_other	1.695	1.333	32
X-RAY DIFFRACTION	r_scangle_it	4.99	2.362	79
X-RAY DIFFRACTION	r_scangle_other	2.385	1.914	52
X-RAY DIFFRACTION	r_lrange_it	2.941	14.319	61
X-RAY DIFFRACTION	r_lrange_other	2.572	12.564	55
X-RAY DIFFRACTION	r_rigid_bond_restr	0.872	3	196

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.122-1.151	0.284	5	0.379	49	0.372	220	0.257	0.383	24.5455	0.374
1.151-1.183	0.311	9	0.336	78	0.334	210	0.509	0.469	41.4286	0.338
1.183-1.217	0.267	12	0.291	108	0.289	188	0.717	0.561	63.8298	0.276
1.217-1.254	0.301	18	0.244	160	0.249	199	0.633	0.68	89.4472	0.229
1.254-1.295	0.127	15	0.231	143	0.22	183	0.863	0.795	86.3388	0.226
1.295-1.34	0.253	15	0.182	134	0.188	186	0.833	0.897	80.1075	0.18
1.34-1.39	0.313	16	0.201	141	0.211	177	0.822	0.901	88.7006	0.188
1.39-1.447	0.3	15	0.149	131	0.165	176	0.885	0.929	82.9545	0.145
1.447-1.511	0.212	13	0.114	124	0.122	157	0.91	0.951	87.2611	0.115
1.511-1.584	0.163	15	0.135	135	0.138	162	0.95	0.945	92.5926	0.132
1.584-1.669	0.162	14	0.137	122	0.14	143	0.956	0.954	95.1049	0.135
1.669-1.77	0.209	12	0.146	107	0.153	134	0.934	0.957	88.806	0.152
1.77-1.891	0.176	13	0.137	116	0.141	147	0.952	0.964	87.7551	0.15
1.891-2.041	0.215	10	0.122	88	0.13	106	0.96	0.972	92.4528	0.138
2.041-2.233	0.112	11	0.104	99	0.105	119	0.98	0.979	92.437	0.126
2.233-2.492	0.19	9	0.131	86	0.136	100	0.968	0.975	95	0.16
2.492-2.87	0.209	9	0.159	81	0.164	94	0.949	0.97	95.7447	0.187
2.87-3.496	0.19	7	0.148	60	0.152	74	0.963	0.976	90.5405	0.164
3.496-4.867	0.183	5	0.138	50	0.142	59	0.987	0.985	93.2203	0.182
4.867-19.469	0.19	4	0.181	30	0.181	34	0.927	0.982	100	0.232

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi