BMRB Entry 19108

Name: NMR structure of human restriction factor APOBEC3A
Published: 2013-05-20

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PDB ID: 2m65
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19108
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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:

NMR structure of human restriction factor APOBEC3A

Deposition date:

2013-03-21

Original release date:

2013-05-20

Authors:

Byeon, In-Ja; Byeon, Chang-Hyeock; Ahn, Jinwoo; Gronenborn, Angela

Citation:

Citation: Byeon, In-Ja; Ahn, Jinwoo; Mitra, Mithun; Byeon, Chang-Hyeock; Hercik, Kamil; Hritz, Jozef; Charlton, Lisa; Levin, Judith; Gronenborn, Angela. "NMR structure of human restriction factor APOBEC3A reveals substrate binding and enzyme specificity." Nat. Commun. 4, 1890-1890 (2013).
PubMed: 23695684

Assembly members:

Assembly members:
entity_1, polymer, 199 residues, 23041.172 Da.
entity_ZN, non-polymer, 65.409 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: pET21

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MEASPASGPRHLMDPHIFTS NFNNGIGRHKTYLCYEVERL DNGTSVKMDQHRGFLHNQAK NLLCGFYGRHAELRFLDLVP SLQLDPAQIYRVTWFISWSP CFSWGCAGEVRAFLQENTHV RLRIFAARIYDYDPLYKEAL QMLRDAGAQVSIMTYDEFKH CWDTFVDHQGCPFQPWDGLD EHSQALSGRLRAILQNQGN

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	502
15N chemical shifts	203
1H chemical shifts	1146

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	human restriction factor APOBEC3A	1
2	ZINC ION	2

Entities:

Entity 1, human restriction factor APOBEC3A 199 residues - 23041.172 Da.

1

MET

GLU

ALA

SER

PRO

ALA

SER

GLY

PRO

ARG

2

HIS

LEU

MET

ASP

PRO

HIS

ILE

PHE

THR

SER

3

ASN

PHE

ASN

GLY

ILE

GLY

ARG

HIS

LYS

4

THR

TYR

LEU

CYS

TYR

GLU

VAL

GLU

ARG

LEU

5

ASP

ASN

GLY

THR

SER

VAL

LYS

MET

ASP

GLN

6

HIS

ARG

GLY

PHE

LEU

HIS

ASN

GLN

ALA

LYS

7

ASN

LEU

CYS

GLY

PHE

TYR

GLY

ARG

HIS

8

ALA

GLU

LEU

ARG

PHE

LEU

ASP

LEU

VAL

PRO

9

SER

LEU

GLN

LEU

ASP

PRO

ALA

GLN

ILE

TYR

10

ARG

VAL

THR

TRP

PHE

ILE

SER

TRP

SER

PRO

11

CYS

PHE

SER

TRP

GLY

CYS

ALA

GLY

GLU

VAL

12

ARG

ALA

PHE

LEU

GLN

GLU

ASN

THR

HIS

VAL

13

ARG

LEU

ARG

ILE

PHE

ALA

ARG

ILE

TYR

14

ASP

TYR

ASP

PRO

LEU

TYR

LYS

GLU

ALA

LEU

15

GLN

MET

LEU

ARG

ASP

ALA

GLY

ALA

GLN

VAL

16

SER

ILE

MET

THR

TYR

ASP

GLU

PHE

LYS

HIS

17

CYS

TRP

ASP

THR

PHE

VAL

ASP

HIS

GLN

GLY

18

CYS

PRO

PHE

GLN

PRO

TRP

ASP

GLY

LEU

ASP

19

GLU

HIS

SER

GLN

ALA

LEU

SER

GLY

ARG

LEU

20

ARG

ALA

ILE

LEU

GLN

ASN

GLN

GLY

ASN

Entity 2, ZINC ION - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: APOBEC3A, [U-13C; U-15N], mM; ZINC ION mM

sample_2: APOBEC3A, [U-13C; U-15N], mM; ZINC ION mM

sample_3: APOBEC3A, [U-13C; U-15N], mM; ZINC ION mM

sample_4: APOBEC3A, [U-13C; U-15N], mM; ZINC ION mM

sample_5: APOBEC3A, [U-13C; U-15N], mM; ZINC ION mM

sample_6: APOBEC3A, [U-13C; U-15N], mM; ZINC ION mM

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: . K

sample_conditions_2: pH: 6.5; pressure: 1 atm; temperature: . K

sample_conditions_3: pH: 6.5; pressure: 1 atm; temperature: . K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HN(CO)CACB	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D simulaneous 1H-13C and 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_2
3D HNCA	sample_2	isotropic	sample_conditions_2
3D HN(CO)CA	sample_2	isotropic	sample_conditions_2
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_2
3D simultaneous 1H-13C and 1H-15N NOESY	sample_2	isotropic	sample_conditions_2
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_3
3D HCCH-TOCSY	sample_3	isotropic	sample_conditions_3
3D simulaneous 1H-13C and 1H-15N NOESY	sample_3	isotropic	sample_conditions_3
2D 1H-15N HSQC	sample_4	isotropic	sample_conditions_1
3D HNCACB	sample_4	isotropic	sample_conditions_1
3D HN(CO)CACB	sample_4	isotropic	sample_conditions_1
3D simultaneous 1H-13C and 1H-15N NOESY	sample_4	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_4	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_5	isotropic	sample_conditions_1
3D simultaneous 1H-13C and 1H-15N NOESY	sample_5	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_5	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_6	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_6	isotropic	sample_conditions_1

Software:

TOPSPIN v2.3 -

NMR spectrometers:

Bruker Avance 900 MHz
Bruker Avance 800 MHz
Bruker Avance 700 MHz
Bruker Avance 600 MHz

PDB	2M65 4XXO
DBJ	BAI46227
EMBL	CAG30279 CAK54381 CAK54680
GB	AAA03706 AAI26417 ADO85886 ADR82854 AIC53372
REF	NP_001180218 NP_663745 XP_001149270 XP_011545340 XP_011545341
SP	P31941
AlphaFold	P31941