BMRB Entry 16983

Name: The solution structure of the PHD3 finger of MLL
Published: 2010-08-12

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PDB ID: 2kyu
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16983
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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:

The solution structure of the PHD3 finger of MLL

Deposition date:

2010-06-08

Original release date:

2010-08-12

Authors:

Park, Sangho; Bushweller, John

Citation:

Citation: Park, Sangho; Osmers, Ute; Raman, Gayathree; Schwantes, Rebecca; Diaz, Manuel; Bushweller, John. "The PHD3 Domain of MLL Acts as a CYP33-Regulated Switch between MLL-Mediated Activation and Repression ." Biochemistry 49, 6576-6586 (2010).
PubMed: 20677832

Assembly members:

Assembly members:
PHD3, polymer, 67 residues, 7719.658 Da.
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: GE Healthcare

Entity Sequences (FASTA):

Entity Sequences (FASTA):
PHD3: GSAKGNFCPLCDKCYDDDDY ESKMMQCGKCDRWVHSKCEN LSDEMYEILSNLPESVAYTC VNCTERH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	262
15N chemical shifts	67
1H chemical shifts	429

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	PHD3	1
2	ZINC ION_1	2
3	ZINC ION_2	2

Entities:

Entity 1, PHD3 67 residues - 7719.658 Da.

1

GLY

SER

ALA

LYS

GLY

ASN

PHE

CYS

PRO

LEU

2

CYS

ASP

LYS

CYS

TYR

ASP

TYR

3

GLU

SER

LYS

MET

GLN

CYS

GLY

LYS

CYS

4

ASP

ARG

TRP

VAL

HIS

SER

LYS

CYS

GLU

ASN

5

LEU

SER

ASP

GLU

MET

TYR

GLU

ILE

LEU

SER

6

ASN

LEU

PRO

GLU

SER

VAL

ALA

TYR

THR

CYS

7

VAL

ASN

CYS

THR

GLU

ARG

HIS

Entity 2, ZINC ION_1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: PHD3, [U-98% 13C; U-98% 15N], 1 mM; ZINC ION 100 uM; potassium phosphate 25 mM; DTT 3 mM; sodium chloride 50 mM; sodium azide 1 mM; H2O 95%; D2O 5%

sample_conditions_1: pH: 6.9; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HNHA	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D TROSY-HNCO	sample_1	isotropic	sample_conditions_1
3D TROSY-HNCO	sample_1	anisotropic	sample_conditions_1

Software:

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

NMR spectrometers:

Varian Avance 600 MHz

PDB	2KU7 2KYU 3LQH 3LQI 3LQJ
DBJ	BAA03407 BAD92745
EMBL	CAA58584
GB	AAA58669 AAA92511 AAB34770 AAM33377 AAQ63624
REF	NP_001074518 NP_005924 XP_003253537 XP_003910832 XP_004052287
SP	Q03164
TPG	DAA22311
AlphaFold	Q03164