BMRB Entry 17165

Name: Prion-like conversion during amyloid formation at atomic resolution
Published: 2011-02-04

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PDB ID: 2xks
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17165
MolProbity Validation Chart

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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Prion-like conversion during amyloid formation at atomic resolution

Deposition date:

2010-09-03

Original release date:

2011-02-04

Authors:

Eichner, Timo; Kalverda, Arnout; Thompson, Gary; Radford, Sheena; Homans, Steve

Citation:

Citation: Eichner, Timo; Kalverda, Arnout; Thompson, Gary; Homans, Steve; Radford, Sheena. "Conformational Conversion during Amyloid Formation at Atomic Resolution" Mol. Cell. 41, 161-172 (2011).
PubMed: 21255727

Assembly members:

Assembly members:
WT, polymer, 100 residues, 11864.3434 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET23a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
WT: MIQRTPKIQVYSRHPAENGK SNFLNCYVSGFHPSDIEVDL LKNGERIEKVEHSDLSFSKD WSFYLLYYTEFTPTEKDEYA CRVNHVTLSQPKIVKWDRDM

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	460
15N chemical shifts	97
1H chemical shifts	711

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	WT	1

Entities:

Entity 1, WT 100 residues - 11864.3434 Da.

1	MET	ILE	GLN	ARG	THR	PRO	LYS	ILE	GLN	VAL
2	TYR	SER	ARG	HIS	PRO	ALA	GLU	ASN	GLY	LYS
3	SER	ASN	PHE	LEU	ASN	CYS	TYR	VAL	SER	GLY
4	PHE	HIS	PRO	SER	ASP	ILE	GLU	VAL	ASP	LEU
5	LEU	LYS	ASN	GLY	GLU	ARG	ILE	GLU	LYS	VAL
6	GLU	HIS	SER	ASP	LEU	SER	PHE	SER	LYS	ASP
7	TRP	SER	PHE	TYR	LEU	LEU	TYR	TYR	THR	GLU
8	PHE	THR	PRO	THR	GLU	LYS	ASP	GLU	TYR	ALA
9	CYS	ARG	VAL	ASN	HIS	VAL	THR	LEU	SER	GLN
10	PRO	LYS	ILE	VAL	LYS	TRP	ASP	ARG	ASP	MET

Samples:

15N13C: WT, [U-100% 13C; U-100% 15N], 0.5 ± 5e-05 mM; sodium phosphate 25.0 ± 0.0025 mM; sodium acide 1.0 ± 0.0001 mM; H2O 90%; D2O 10%

15N13C_d2o: WT, [U-100% 13C; U-100% 15N], 0.3 ± 3e-05 mM; sodium phosphate 25.0 ± 0.0025 mM; sodium acide 1.0 ± 0.0001 mM; D2O 100%

Structure: ionic strength: 0.040 M; pH: 7.500; pressure: 1.000 atm; temperature: 298.000 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC/HMQC	15N13C	isotropic	Structure
3D HNCA	15N13C	isotropic	Structure
CBCACONH (H[N[co[{CA\|ca[C]}]]])	15N13C	isotropic	Structure
3D HNCO	15N13C	isotropic	Structure
HCCONH (HccoNH)	15N13C	isotropic	Structure
CCONH (hC_ccoNH.TOCSY)	15N13C	isotropic	Structure
3D HN(CO)CA	15N13C	isotropic	Structure
3D HNCACB	15N13C	isotropic	Structure
3D HCCH-TOCSY	15N13C	isotropic	Structure
3D HCCH-COSY	15N13C	isotropic	Structure
C_TOCSY (hC_CH.TOCSY)	15N13C	isotropic	Structure
3D 1H-15N NOESY	15N13C	isotropic	Structure
2D 1H-13C HSQC/HMQC	15N13C_d2o	isotropic	Structure
2D 1H-13C HSQC/HMQC	15N13C_d2o	isotropic	Structure
2D 1H-13C HSQC/HMQC	15N13C_d2o	isotropic	Structure
3D 1H-13C NOESY	15N13C_d2o	isotropic	Structure
3D 1H-13C NOESY	15N13C_d2o	isotropic	Structure
CBCACONH	15N13C_d2o	solution	Structure
CCONH	15N13C_d2o	solution	Structure

Software:

ARIA v2.1, Linge, O'Donoghue and Nilges - refinement

AutoDep v4.3, PDBe - collection

ANALYSIS v2.1, CCPN - data analysis

NMRPipe v2.5, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView v5.22, Johnson, One Moon Scientific - data analysis

PASD_algorithm v1.0, Kuszewski et al. - de novo structure calculation

VNMR v6.1c, VARIAN - collection

VNMR_6.1C vany, Varian - collection

X-PLOR NIH v2.17, Schwieters, Kusyewski, Tjandra and Clore - structure solution

NMR spectrometers:

Varian INOVA 500 MHz
Varian INOVA 749 MHz
Varian INOVA 600 MHz
Varian IVANOVA 500 MHz

Related Database Links:

UNP	B2MG_HUMAN
BMRB	15480 16587 17166 19099 19113 19116 19118 19119 19120 19121 19122 19123 3078 3079
PDB	1A1M 1A1N 1A1O 1A6Z 1A9B 1A9E 1AGB 1AGC 1AGD 1AGE 1AGF 1AKJ 1AO7 1B0G 1B0R 1BD2 1C16 1CE6 1CG9 1DE4 1DUY 1DUZ 1E27 1E28 1EEY 1EEZ 1EFX 1EXU 1GZP 1GZQ 1HHG 1HHH 1HHI 1HHJ 1HHK 1HLA 1HSA 1HSB 1I1F 1I1Y 1I4F 1I7R 1I7T 1I7U 1IM3 1IM9 1JF1 1JGD 1JGE 1JHT 1JNJ 1K5N 1KPR 1KTL 1LDS 1LP9 1M05 1M6O 1MHE 1MI5 1N2R 1OF2 1OGA 1OGT 1ONQ 1P7Q 1PY4 1Q94 1QEW 1QLF 1QQD 1QR1 1QRN 1QSE 1QSF 1QVO 1R3H 1S8D 1S9W 1S9X 1S9Y 1SYS 1SYV 1T1W 1T1X 1T1Y 1T1Z 1T20 1T21 1T22 1TMC 1TVB 1TVH 1UQS 1UXS 1UXW 1VGK 1W0V 1W0W 1W72 1X7Q 1XH3 1XR8 1XR9 1XZ0 1YDP 1YPZ 1ZHK 1ZHL 1ZS8 1ZSD 1ZT4 1ZVS 2A83 2AK4 2AV1 2AV7 2AXF 2AXG 2BCK 2BNQ 2BNR 2BSR 2BSS 2BST 2BVO 2BVP 2BVQ 2C7U 2CII 2CIK 2CLR 2D31 2D4D 2D4F 2DYP 2ESV 2F53 2F54 2F74 2F8O 2FYY 2FZ3 2GIT 2GJ6 2GT9 2GTW 2GTZ 2GUO 2H26 2H6P 2HJK 2HJL 2HLA 2HN7 2J8U 2JCC 2NW3 2NX5 2P5E 2P5W 2PO6 2PYE 2RFX 2UWE 2V2W 2V2X 2VB5 2VLJ 2VLK 2VLL 2VLR 2X4N 2X4O 2X4P 2X4Q 2X4R 2X4S 2X4T 2X4U 2X70 2X89 2XKS 2XKU 2XPG 2YPK 2YPL 2YXF 2Z9T 3AM8 3B3I 3B6S 3BGM 3BH8 3BH9 3BHB 3BO8 3BP4 3BP7 3BVN 3BW9 3BWA 3BXN 3BZE 3BZF 3C9N 3CDG 3CII 3CIQ 3CZF 3D18 3D25 3D2U 3D39 3D3V 3DBX 3DHJ 3DHM 3DTX 3DX6 3DX7 3DX8 3DXA 3EKC 3FFC 3FQN 3FQR 3FQT 3FQU 3FQW 3FQX 3FT2 3FT3 3FT4 3GIV 3GJF 3GSN 3GSO 3GSQ 3GSR 3GSU 3GSV 3GSW 3GSX 3H7B 3H9H 3H9S 3HAE 3HCV 3HG1 3HLA 3HPJ 3HUJ 3I6G 3I6K 3I6L 3IB4 3IXA 3JTS 3KLA 3KPL 3KPM 3KPN 3KPO 3KPP 3KPQ 3KPR 3KPS 3KWW 3KXF 3KYN 3KYO 3L3D 3L3G 3L3I 3L3J 3L3K 3LKN 3LKO 3LKP 3LKQ 3LKR 3LKS 3LN4 3LN5 3LOW 3LV3 3M17 3M1B 3MGO 3MGT 3MR9 3MRB 3MRC 3MRD 3MRE 3MRF 3MRG 3MRH 3MRI 3MRJ 3MRK 3MRL 3MRM 3MRN 3MRO 3MRP 3MRQ 3MRR 3MV7 3MV8 3MV9 3MYJ 3MYZ 3MZT 3NA4 3NFN 3O3A 3O3B 3O3D 3O3E 3O4L 3OV6 3OX8 3OXR 3OXS 3PWJ 3PWL 3PWN 3PWP 3QDA 3QDG 3QDJ 3QDM 3QEQ 3QFD 3QFJ 3QZW 3REW 3RL1 3RL2 3RWJ 3SDX 3SJV 3SKM 3SKO 3SPV 3T8X 3TID 3TIE 3TLR 3TM6 3TO2 3TZV 3U0P 3UPR 3UTQ 3UTS 3UTT 3V5D 3V5H 3V5K 3VCL 3VFM 3VFN 3VFO 3VFP 3VFR 3VFS 3VFT 3VFU 3VFV 3VFW 3VH8 3VRI 3VRJ 3VWJ 3VWK 3VXM 3VXN 3VXO 3VXP 3VXR 3VXS 3VXU 3W0W 3W39 3WL9 3WLB 3WUW 4E5X 4EN3 4EUP 4F7M 4F7P 4F7T 4FTV 4FXL 4G8G 4G8I 4G9D 4G9F 4GKN 4GKS 4GUP 4HKJ 4HWZ 4HX1 4I48 4I4W 4JFD 4JFE 4JFF 4JFO 4JFP 4JFQ 4JQV 4JQX 4JRX 4JRY 4K71 4K7F 4KDT 4L29 4L3C 4L3E 4L4T 4L4V 4LCW 4LCY 4LHU 4LNR 4M8V 4MJ5 4MJ6 4MJI 4MNQ 4N0F 4N0U 4N8V 4NNX 4NNY 4NO0 4NO2 4NQC 4NQD 4NQE 4NQV 4NQX 4NT6 4O2C 4O2E 4O2F 4ONO 4PJ5 4PJ7 4PJ8 4PJ9 4PJA 4PJB 4PJC 4PJD 4PJE 4PJF 4PJG 4PJH 4PJI 4PJX 4PR5 4PRA 4PRB 4PRD 4PRE 4PRH 4PRI 4PRN 4PRP 4QOK 4QRP 4QRQ 4QRR 4QRS 4QRT 4QRU 4R9H 4RA3 4RAH 4U1H 4U1I 4U1J 4U1K 4U1L 4U1M 4U1N 4U1S 4U6X 4U6Y 4UQ2 4UQ3 4WDI 4WJ5 4WO4 4WU5 4WU7 4X6C 4X6D 4X6E 4X6F 4XXC 4Z76 4Z77 4Z78 5BXF
DBJ	BAA35182 BAG38125 BAG64583 BAG72952
EMBL	CAA23830 CAG33347 CAH92078
GB	AAA51811 AAA87972 AAA88008 AAB25312 AAB35347
REF	NP_001009066 NP_001127503 NP_004039 XP_003266898 XP_004056148
SP	P16213 P61769 P61770 P61771
AlphaFold	Q9UDF4 P16213 P61769 P61770 P61771

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks

1	MET	ILE	GLN	ARG	THR	PRO	LYS	ILE	GLN	VAL
2	TYR	SER	ARG	HIS	PRO	ALA	GLU	ASN	GLY	LYS
3	SER	ASN	PHE	LEU	ASN	CYS	TYR	VAL	SER	GLY
4	PHE	HIS	PRO	SER	ASP	ILE	GLU	VAL	ASP	LEU
5	LEU	LYS	ASN	GLY	GLU	ARG	ILE	GLU	LYS	VAL
6	GLU	HIS	SER	ASP	LEU	SER	PHE	SER	LYS	ASP
7	TRP	SER	PHE	TYR	LEU	LEU	TYR	TYR	THR	GLU
8	PHE	THR	PRO	THR	GLU	LYS	ASP	GLU	TYR	ALA
9	CYS	ARG	VAL	ASN	HIS	VAL	THR	LEU	SER	GLN
10	PRO	LYS	ILE	VAL	LYS	TRP	ASP	ARG	ASP	MET

1	MET	ILE	GLN	ARG	THR	PRO	LYS	ILE	GLN	VAL
2	TYR	SER	ARG	HIS	PRO	ALA	GLU	ASN	GLY	LYS
3	SER	ASN	PHE	LEU	ASN	CYS	TYR	VAL	SER	GLY
4	PHE	HIS	PRO	SER	ASP	ILE	GLU	VAL	ASP	LEU
5	LEU	LYS	ASN	GLY	GLU	ARG	ILE	GLU	LYS	VAL
6	GLU	HIS	SER	ASP	LEU	SER	PHE	SER	LYS	ASP
7	TRP	SER	PHE	TYR	LEU	LEU	TYR	TYR	THR	GLU
8	PHE	THR	PRO	THR	GLU	LYS	ASP	GLU	TYR	ALA
9	CYS	ARG	VAL	ASN	HIS	VAL	THR	LEU	SER	GLN
10	PRO	LYS	ILE	VAL	LYS	TRP	ASP	ARG	ASP	MET

1	MET	ILE	GLN	ARG	THR	PRO	LYS	ILE	GLN	VAL
2	TYR	SER	ARG	HIS	PRO	ALA	GLU	ASN	GLY	LYS
3	SER	ASN	PHE	LEU	ASN	CYS	TYR	VAL	SER	GLY
4	PHE	HIS	PRO	SER	ASP	ILE	GLU	VAL	ASP	LEU
5	LEU	LYS	ASN	GLY	GLU	ARG	ILE	GLU	LYS	VAL
6	GLU	HIS	SER	ASP	LEU	SER	PHE	SER	LYS	ASP
7	TRP	SER	PHE	TYR	LEU	LEU	TYR	TYR	THR	GLU
8	PHE	THR	PRO	THR	GLU	LYS	ASP	GLU	TYR	ALA
9	CYS	ARG	VAL	ASN	HIS	VAL	THR	LEU	SER	GLN
10	PRO	LYS	ILE	VAL	LYS	TRP	ASP	ARG	ASP	MET