BMRB Entry 25509

Name: 1H, 13C, 15N chemical shift assignments for APOBEC3G NTD variant, sNTD
Published: 2015-05-05

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PDB ID: 2mzz
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25509
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

1H, 13C, 15N chemical shift assignments for APOBEC3G NTD variant, sNTD

Deposition date:

2015-02-28

Original release date:

2015-05-05

Authors:

Kouno, Takahide; Luengas, Elizabeth; Shigematu, Megumi; Shandilya, Shivender; Zhang, JingYing; Chen, Luan; Hara, Mayuko; Schiffer, Celia; Harris, Reuben; Matsuo, Hiroshi

Citation:

Citation: Kono, Takahide; Luengas, Elizabeth; Shigematu, Megumi; Shandilya, Shivender; Zhang, JingYing; Chen, Luan; Hara, Mayuko; Schiffer, Celia; Harris, Reuben; Matsuo, Hiroshi. "Structure of the Vif-binding domain of the antiviral enzyme APOBEC3G" Nat. Struct. Mol. Biol. ., .-..

Assembly members:

Assembly members:
sNTD, polymer, 180 residues, 21316.219 Da.
ZINC ION, non-polymer, 65.409 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pCold-GST

Entity Sequences (FASTA):

Entity Sequences (FASTA):
sNTD: MDPDTFSYNFNNRPILSRRN TVWLCYEVKTKGPSRPPLDA KIFRGQVYSEDKYHPEMRFL SLVSKWKLHRDQEYEVTWYI SWSPCTKCARDMATFLQENT HVTLTIFVARLYYAWDPDYQ EALRSLAQAGATIKIMNYDE FQHCWSKFVYSQGAPFQPWD GLDEHSQALSGRLGEILRHS

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	317
15N chemical shifts	147
1H chemical shifts	289

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity	1
2	ZINC ION	2

Entities:

Entity 1, entity 180 residues - 21316.219 Da.

1	MET	ASP	PRO	ASP	THR	PHE	SER	TYR	ASN	PHE
2	ASN	ASN	ARG	PRO	ILE	LEU	SER	ARG	ARG	ASN
3	THR	VAL	TRP	LEU	CYS	TYR	GLU	VAL	LYS	THR
4	LYS	GLY	PRO	SER	ARG	PRO	PRO	LEU	ASP	ALA
5	LYS	ILE	PHE	ARG	GLY	GLN	VAL	TYR	SER	GLU
6	ASP	LYS	TYR	HIS	PRO	GLU	MET	ARG	PHE	LEU
7	SER	LEU	VAL	SER	LYS	TRP	LYS	LEU	HIS	ARG
8	ASP	GLN	GLU	TYR	GLU	VAL	THR	TRP	TYR	ILE
9	SER	TRP	SER	PRO	CYS	THR	LYS	CYS	ALA	ARG
10	ASP	MET	ALA	THR	PHE	LEU	GLN	GLU	ASN	THR
11	HIS	VAL	THR	LEU	THR	ILE	PHE	VAL	ALA	ARG
12	LEU	TYR	TYR	ALA	TRP	ASP	PRO	ASP	TYR	GLN
13	GLU	ALA	LEU	ARG	SER	LEU	ALA	GLN	ALA	GLY
14	ALA	THR	ILE	LYS	ILE	MET	ASN	TYR	ASP	GLU
15	PHE	GLN	HIS	CYS	TRP	SER	LYS	PHE	VAL	TYR
16	SER	GLN	GLY	ALA	PRO	PHE	GLN	PRO	TRP	ASP
17	GLY	LEU	ASP	GLU	HIS	SER	GLN	ALA	LEU	SER
18	GLY	ARG	LEU	GLY	GLU	ILE	LEU	ARG	HIS	SER

Entity 2, ZINC ION - 65.409 Da.

1

ZN

Samples:

sample_1: entity, [U-100% 15N; U-85% 2H], 0.15-0.20 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; H2O 95%; D2O 5%

sample_2: entity, [U-100% 13C; U-100% 15N; U-85% 2H], 0.15-0.20 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; H2O 95%; D2O 5%

sample_3: entity, [U-100% 13C; U-100% 15N; U-60% 2H], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; H2O 95%; D2O 5%

sample_4: entity, [U-80% 2H; 100% 15N-Arg], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; H2O 95%; D2O 5%

sample_5: entity, [U-80% 2H; 100% 15N-Ile], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; H2O 95%; D2O 5%

sample_6: entity, [U-80% 2H; 100% 15N-Leu], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; H2O 95%; D2O 5%

sample_7: entity, [U-80% 2H; 100% 15N-Lys], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; H2O 95%; D2O 5%

sample_8: entity, [U-80% 2H; 100% 15N-Phe], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; H2O 95%; D2O 5%

sample_9: entity, [U-80% 2H; 100% 15N-Tyr], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; H2O 95%; D2O 5%

sample_10: entity, [U-80% 2H; 100% 1H, 100% 13C-Ala], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; H2O 95%; D2O 5%

sample_11: entity, [U-80% 2H; 100% 1H, 100% 13C-Arg], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; D2O 100%

sample_12: entity, [U-80% 2H; 100% 1H, 100% 13C-Ile], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; D2O 100%

sample_13: entity, [U-80% 2H; 100% 1H, 100% 13C-Leu], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; D2O 100%

sample_14: entity, [U-80% 2H; 100% 1H, 100% 13C-Lys], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; D2O 100%

sample_15: entity, [U-80% 2H; 100% 1H, 100% 13C-Met], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; D2O 100%

sample_16: entity, [U-80% 2H; 100% 1H, 100% 13C-Phe], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; D2O 100%

sample_17: entity, [U-80% 2H; 100% 1H, 100% 13C-Thr], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; D2O 100%

sample_18: entity, [U-80% 2H; 100% 1H, 100% 13C-Tyr], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; D2O 100%

sample_19: entity, [U-80% 2H; 100% 1H, 100% 13C-Val], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; D2O 100%

sample_20: entity, [U-80% 2H; 100% 1H-Phe,Tyr,Ile], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; D2O 100%

sample_21: entity, [U-80% 2H; 100% 1H-Phe,Tyr,Leu], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; D2O 100%

sample_22: entity, [U-80% 2H; 100% 1H-Phe,Tyr,Val], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; D2O 100%

sample_23: entity, [U-80% 2H; 100% 1H-Trp,Ile,Leu,Val], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; D2O 100%

sample_24: entity 0.15-0.20 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; D2O 100%

condition_1: pH: 7.3; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N TROSY	sample_1	isotropic	condition_1
3D HNCA-TROSY	sample_2	isotropic	condition_1
3D HN(CO)CA-TROSY	sample_2	isotropic	condition_1
3D HNCO-TROSY	sample_2	isotropic	condition_1
3D HN(CA)CO-TROSY	sample_2	isotropic	condition_1
3D HNCACB-TROSY	sample_2	isotropic	condition_1
3D HN(CO)CACB-TROSY	sample_2	isotropic	condition_1
3D 15N-edited NOESY	sample_3	isotropic	condition_1
2D 1H-15N TROSY	sample_4	isotropic	condition_1
2D 1H-15N TROSY	sample_5	isotropic	condition_1
2D 1H-15N TROSY	sample_6	isotropic	condition_1
2D 1H-15N TROSY	sample_7	isotropic	condition_1
2D 1H-15N TROSY	sample_8	isotropic	condition_1
2D 1H-15N TROSY	sample_9	isotropic	condition_1
2D 1H-13C HSQC	sample_10	isotropic	condition_1
2D 1H-13C HSQC	sample_11	isotropic	condition_1
2D 1H-13C HSQC	sample_12	isotropic	condition_1
2D 1H-13C HSQC	sample_13	isotropic	condition_1
2D 1H-13C HSQC	sample_14	isotropic	condition_1
2D 1H-13C HSQC	sample_15	isotropic	condition_1
2D 1H-13C HSQC	sample_16	isotropic	condition_1
2D 1H-13C HSQC	sample_17	isotropic	condition_1
2D 1H-13C HSQC	sample_18	isotropic	condition_1
2D 1H-13C HSQC	sample_19	isotropic	condition_1
2D 1H-1H NOESY	sample_10	isotropic	condition_1
2D 1H-1H NOESY	sample_11	isotropic	condition_1
2D 1H-1H NOESY	sample_12	isotropic	condition_1
2D 1H-1H NOESY	sample_13	isotropic	condition_1
2D 1H-1H NOESY	sample_14	isotropic	condition_1
2D 1H-1H NOESY	sample_15	isotropic	condition_1
2D 1H-1H NOESY	sample_16	isotropic	condition_1
2D 1H-1H NOESY	sample_17	isotropic	condition_1
2D 1H-1H NOESY	sample_18	isotropic	condition_1
2D 1H-1H NOESY	sample_19	isotropic	condition_1
2D 1H-1H NOESY	sample_20	isotropic	condition_1
2D 1H-1H NOESY	sample_21	isotropic	condition_1
2D 1H-1H NOESY	sample_22	isotropic	condition_1
2D 1H-1H NOESY	sample_23	isotropic	condition_1
2D 1H-1H NOESY	sample_24	isotropic	condition_1
3D 1H-13C NOESY	sample_3	isotropic	condition_1

Software:

TOPSPIN, Bruker Biospin - collection

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY, Goddard - data analysis

TALOS, Cornilescu, Delaglio and Bax - estimation of dihedral angles

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution

Molmol, Koradi, Billeter and Wuthrich - drawing structures

MacPyMol, Schrodinger - drawing structures

ProcheckNMR, Laskowski and MacArthur - evaluation of structure quality

NMR spectrometers:

Bruker Avance 700 MHz
Bruker Avance 850 MHz
Bruker Avance 900 MHz

1	MET	ASP	PRO	ASP	THR	PHE	SER	TYR	ASN	PHE
2	ASN	ASN	ARG	PRO	ILE	LEU	SER	ARG	ARG	ASN
3	THR	VAL	TRP	LEU	CYS	TYR	GLU	VAL	LYS	THR
4	LYS	GLY	PRO	SER	ARG	PRO	PRO	LEU	ASP	ALA
5	LYS	ILE	PHE	ARG	GLY	GLN	VAL	TYR	SER	GLU
6	ASP	LYS	TYR	HIS	PRO	GLU	MET	ARG	PHE	LEU
7	SER	LEU	VAL	SER	LYS	TRP	LYS	LEU	HIS	ARG
8	ASP	GLN	GLU	TYR	GLU	VAL	THR	TRP	TYR	ILE
9	SER	TRP	SER	PRO	CYS	THR	LYS	CYS	ALA	ARG
10	ASP	MET	ALA	THR	PHE	LEU	GLN	GLU	ASN	THR
11	HIS	VAL	THR	LEU	THR	ILE	PHE	VAL	ALA	ARG
12	LEU	TYR	TYR	ALA	TRP	ASP	PRO	ASP	TYR	GLN
13	GLU	ALA	LEU	ARG	SER	LEU	ALA	GLN	ALA	GLY
14	ALA	THR	ILE	LYS	ILE	MET	ASN	TYR	ASP	GLU
15	PHE	GLN	HIS	CYS	TRP	SER	LYS	PHE	VAL	TYR
16	SER	GLN	GLY	ALA	PRO	PHE	GLN	PRO	TRP	ASP
17	GLY	LEU	ASP	GLU	HIS	SER	GLN	ALA	LEU	SER
18	GLY	ARG	LEU	GLY	GLU	ILE	LEU	ARG	HIS	SER

1	MET	ASP	PRO	ASP	THR	PHE	SER	TYR	ASN	PHE
2	ASN	ASN	ARG	PRO	ILE	LEU	SER	ARG	ARG	ASN
3	THR	VAL	TRP	LEU	CYS	TYR	GLU	VAL	LYS	THR
4	LYS	GLY	PRO	SER	ARG	PRO	PRO	LEU	ASP	ALA
5	LYS	ILE	PHE	ARG	GLY	GLN	VAL	TYR	SER	GLU
6	ASP	LYS	TYR	HIS	PRO	GLU	MET	ARG	PHE	LEU
7	SER	LEU	VAL	SER	LYS	TRP	LYS	LEU	HIS	ARG
8	ASP	GLN	GLU	TYR	GLU	VAL	THR	TRP	TYR	ILE
9	SER	TRP	SER	PRO	CYS	THR	LYS	CYS	ALA	ARG
10	ASP	MET	ALA	THR	PHE	LEU	GLN	GLU	ASN	THR
11	HIS	VAL	THR	LEU	THR	ILE	PHE	VAL	ALA	ARG
12	LEU	TYR	TYR	ALA	TRP	ASP	PRO	ASP	TYR	GLN
13	GLU	ALA	LEU	ARG	SER	LEU	ALA	GLN	ALA	GLY
14	ALA	THR	ILE	LYS	ILE	MET	ASN	TYR	ASP	GLU
15	PHE	GLN	HIS	CYS	TRP	SER	LYS	PHE	VAL	TYR
16	SER	GLN	GLY	ALA	PRO	PHE	GLN	PRO	TRP	ASP
17	GLY	LEU	ASP	GLU	HIS	SER	GLN	ALA	LEU	SER
18	GLY	ARG	LEU	GLY	GLU	ILE	LEU	ARG	HIS	SER