BMRB Entry 34727

Name: RNA binding induces an allosteric switch in Cyp33 to repress MLL1 mediated transcription
Published: 2022-04-11

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PDB ID: 7zey
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34727
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:

RNA binding induces an allosteric switch in Cyp33 to repress MLL1 mediated transcription

Deposition date:

2022-03-31

Original release date:

2022-04-11

Authors:

Blatter, M.; Allain, F.; Meylan, C.

Citation:

Citation: Blatter, Markus; Meylan, Charlotte; Clery, Antoine; Giambruno, Roberto; Nikolaev, Yaroslav; Heidecker, Michel; Solanki, Jessica Arvindbhai; Diaz, Manuel; Gabellini, Davide; Allain, Frederic H-T. "RNA binding induces an allosteric switch in Cyp33 to repress MLL1-mediated transcription" Sci. Adv. 9, eadf5330-eadf5330 (2023).
PubMed: 37075125

Assembly members:

Assembly members:
entity_1, polymer, 117 residues, 13189.849 Da.
entity_2, polymer, 64 residues, 7437.360 Da.
entity_ZN, non-polymer, 65.409 Da.

Natural source:

Natural source: Common Name: human Taxonomy ID: 9606 Superkingdom: not available Kingdom: not available Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: PTYB12

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: AGHMATTKRVLYVGGLAEEV DDKVLHAAFIPFGDITDIQI PLDYETEKHRGFAFVEFELA EDAAAAIDNMNESELFGRTI RVNLAKPMRIKEGSSRPVWS DDDWLKKFSGKTLEENK
entity_2: AKGNFCPLCDKCYDDDDYES KMMQCGKCDRWVHSKCENLS DEMYEILSNLPESVAYTCVN CTER

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
- assigned_chemical_shifts_2

Data type	Count
13C chemical shifts	547
15N chemical shifts	173
1H chemical shifts	1152

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	2
3	unit_3	3
4	unit_4	3

Entities:

Entity 1, unit_1 117 residues - 13189.849 Da.

1

ALA

GLY

HIS

MET

ALA

THR

LYS

ARG

VAL

2

LEU

TYR

VAL

GLY

LEU

ALA

GLU

VAL

3

ASP

LYS

VAL

LEU

HIS

ALA

PHE

ILE

4

PRO

PHE

GLY

ASP

ILE

THR

ASP

ILE

GLN

ILE

5

PRO

LEU

ASP

TYR

GLU

THR

GLU

LYS

HIS

ARG

6

GLY

PHE

ALA

PHE

VAL

GLU

PHE

GLU

LEU

ALA

7

GLU

ASP

ALA

ILE

ASP

ASN

MET

8

ASN

GLU

SER

GLU

LEU

PHE

GLY

ARG

THR

ILE

9

ARG

VAL

ASN

LEU

ALA

LYS

PRO

MET

ARG

ILE

10

LYS

GLU

GLY

SER

ARG

PRO

VAL

TRP

SER

11

ASP

TRP

LEU

LYS

PHE

SER

GLY

12

LYS

THR

LEU

GLU

ASN

LYS

Entity 2, unit_2 64 residues - 7437.360 Da.

1

ALA

LYS

GLY

ASN

PHE

CYS

PRO

LEU

CYS

ASP

2

LYS

CYS

TYR

ASP

TYR

GLU

SER

3

LYS

MET

GLN

CYS

GLY

LYS

CYS

ASP

ARG

4

TRP

VAL

HIS

SER

LYS

CYS

GLU

ASN

LEU

SER

5

ASP

GLU

MET

TYR

GLU

ILE

LEU

SER

ASN

LEU

6

PRO

GLU

SER

VAL

ALA

TYR

THR

CYS

VAL

ASN

7

CYS

THR

GLU

ARG

Entity 3, unit_3 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, [U-100% 15N], 1 mM; HISTONE-LYSINE N-METHYLTRANSFERASE 2A, [U-100% 15N], 1 mM; sodium chloride 40 mM; sodium phosphate 40 mM; zinc chloride 50 uM

sample_2: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, [U-100% 13C; U-100% 15N], 1 mM; HISTONE-LYSINE N-METHYLTRANSFERASE 2A, [U-100% 13C; U-100% 15N], 1 mM; sodium chloride 40 mM; sodium phosphate 40 mM; zinc chloride 50 uM

sample_3: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, [U-100% 13C; U-100% 15N], 1 mM; HISTONE-LYSINE N-METHYLTRANSFERASE 2A 1 mM; sodium chloride 40 mM; sodium phosphate 40 mM; zinc chloride 50 uM

sample_4: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E 1 mM; HISTONE-LYSINE N-METHYLTRANSFERASE 2A, [U-100% 13C; U-100% 15N], 1 mM; sodium chloride 40 mM; sodium phosphate 40 mM; zinc chloride 50 uM

sample_conditions_1: ionic strength: 80 mM; pH: 7; pressure: 1 atm; temperature: 310.15 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_2	isotropic	sample_conditions_1
3D F3-FILTERED- F2-EDITED 13C NOESY	sample_3	isotropic	sample_conditions_1
3D F3-FILTERED- F2-EDITED 13C NOESY	sample_4	isotropic	sample_conditions_1
2D F2- FILTERED NOESY	sample_4	isotropic	sample_conditions_1
2D F2- FILTERED NOESY	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_4	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_4	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_4	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_4	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_3	isotropic	sample_conditions_1

Software:

Amber, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

Sparky, Goddard - chemical shift assignment, peak picking

NMR spectrometers:

Bruker AVANCE III 900 MHz
Bruker AVANCE III 700 MHz

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