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Found 1 Document (2.237 seconds)

BMRB: 25423

2MXP

Solution structure of NDP52 ubiquitin-binding zinc finger

Authors

Pan, L., Xie, X.

Assembly

NDP52 ubiquitin-binding zinc finger

Entity

1. NDP52 ubiquitin-binding zinc finger, entity 1 (polymer, Thiol state: free and other bound), 33 monomers, 3883.512 Da Detail

QMQPLCFNCP ICDKIFPATE KQIFEDHVFC HSL

2. ZINC ION (non-polymer), 65.409 Da

Total weight

3948.921 Da

Max. entity weight

3883.512 Da

Entity Connection

metal coordination 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	metal coordination	sing	1:HIS27:NE2	2:ZN1:ZN
2	metal coordination	sing	1:HIS31:NE2	2:ZN1:ZN
3	metal coordination	sing	1:CYS12:SG	2:ZN1:ZN
4	metal coordination	sing	1:CYS9:SG	2:ZN1:ZN

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 82.6 %, Completeness (bb): 80.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	82.6 % (336 of 407)	94.4 % (201 of 213)	63.1 % (101 of 160)	100.0 % (34 of 34)
Backbone	80.2 % (154 of 192)	93.7 % (59 of 63)	65.7 % (65 of 99)	100.0 % (30 of 30)
Sidechain	86.3 % (214 of 248)	94.7 % (142 of 150)	72.3 % (68 of 94)	100.0 % (4 of 4)
Aromatic	45.8 % (22 of 48)	91.7 % (22 of 24)	0.0 % (0 of 24)
Methyl	100.0 % (28 of 28)	100.0 % (14 of 14)	100.0 % (14 of 14)

1. entity 1

QMQPLCFNCP ICDKIFPATE KQIFEDHVFC HSL

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 2 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	1 mM
2	entity_1	[U-100% 15N]	1 mM
3	D2O	natural abundance	10 %
4	H2O	natural abundance	90 %
5	Potassium phosphate buffer	natural abundance	50 mM
6	NaCl	natural abundance	50 mM
7	DTT	natural abundance	1 mM

Sample #2

Solvent system 100% D2O, Pressure 2 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	entity_1	[U-100% 13C; U-100% 15N]	1 mM
9	D2O	natural abundance	100 %
10	Potassium phosphate buffer	natural abundance	50 mM
11	NaCl	natural abundance	50 mM
12	DTT	natural abundance	1 mM

Sample #3

Solvent system 100% D2O, Pressure 2 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
13	entity_1	natural abundance	1.2 mM
14	D2O	natural abundance	100 %
15	Potassium phosphate buffer	natural abundance	50 mM
16	NaCl	natural abundance	50 mM
17	DTT	natural abundance	1 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2MXP, Strand ID: A Detail

Release date

2015-11-08

Citation

Molecular basis of ubiquitin recognition by the autophagy receptor CALCOCO2
Xie, X., Wang, Y., Lin, Z., Chen, X., Liu, J., Pan, L.
Autophagy (2015), 11, 1775-1789, PubMed 26506893 , DOI 10.1080/15548627.2015.1082025 , Abstract

Related entities 1. NDP52 ubiquitin-binding zinc finger, entity 1, : 2 : 2 : 17 entities Detail

Interaction partners 1. NDP52 ubiquitin-binding zinc finger, entity 1, : 149 interactors Detail

More details for 149 interactors identified by 16 citations

Experiments performed 7 experiments Detail

1 3D CBCA(CO)NH

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	1 mM
2	entity_1	[U-100% 15N]	1 mM
3	D2O	natural abundance	10 %
4	H2O	natural abundance	90 %
5	Potassium phosphate buffer	natural abundance	50 mM
6	NaCl	natural abundance	50 mM
7	DTT	natural abundance	1 mM

2 3D HNCACB

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	1 mM
2	entity_1	[U-100% 15N]	1 mM
3	D2O	natural abundance	10 %
4	H2O	natural abundance	90 %
5	Potassium phosphate buffer	natural abundance	50 mM
6	NaCl	natural abundance	50 mM
7	DTT	natural abundance	1 mM

3 3D 1H-15N NOESY

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	1 mM
2	entity_1	[U-100% 15N]	1 mM
3	D2O	natural abundance	10 %
4	H2O	natural abundance	90 %
5	Potassium phosphate buffer	natural abundance	50 mM
6	NaCl	natural abundance	50 mM
7	DTT	natural abundance	1 mM

4 2D 1H-13C HSQC

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	1 mM
2	entity_1	[U-100% 15N]	1 mM
3	D2O	natural abundance	10 %
4	H2O	natural abundance	90 %
5	Potassium phosphate buffer	natural abundance	50 mM
6	NaCl	natural abundance	50 mM
7	DTT	natural abundance	1 mM

5 3D HCCH-TOCSY

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 2 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	entity_1	[U-100% 13C; U-100% 15N]	1 mM
9	D2O	natural abundance	100 %
10	Potassium phosphate buffer	natural abundance	50 mM
11	NaCl	natural abundance	50 mM
12	DTT	natural abundance	1 mM

6 3D 1H-13C NOESY aliphatic

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 2 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	entity_1	[U-100% 13C; U-100% 15N]	1 mM
9	D2O	natural abundance	100 %
10	Potassium phosphate buffer	natural abundance	50 mM
11	NaCl	natural abundance	50 mM
12	DTT	natural abundance	1 mM

7 2D 1H-1H NOESY

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 2 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
13	entity_1	natural abundance	1.2 mM
14	D2O	natural abundance	100 %
15	Potassium phosphate buffer	natural abundance	50 mM
16	NaCl	natural abundance	50 mM
17	DTT	natural abundance	1 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25423_2mxp.nef
Input source #2: Coordindates	2mxp.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:27:HIS:NE2	2:1:ZN:ZN	unknown	unknown	n/a
1:31:HIS:NE2	2:1:ZN:ZN	unknown	unknown	n/a
1:12:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:9:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	ZN	ZINC ION	None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

-50-------60--------70--------80-
QMQPLCFNCPICDKIFPATEKQIFEDHVFCHSL
|||||||||||||||||||||||||||||||||
QMQPLCFNCPICDKIFPATEKQIFEDHVFCHSL
--------10--------20--------30---

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	33	0	0	100.0

Content subtype: combined_25423_2mxp.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	348		100.0 (chain: A, length: 33)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1333 (1)	noe	100.0 (chain: A, length: 33)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	22 (1)	hbond	45.5 (chain: A, length: 33)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	34 (34)	.	66.7 (chain: A, length: 33)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 33, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 211
  - ¹³C chemical shifts: 103
  - ¹⁵N chemical shifts: 34
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	213	210	98.6
¹³C chemical shifts	160	103	64.4
¹⁵N chemical shifts	34	34	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	63	62	98.4
¹³C chemical shifts	66	33	50.0
¹⁵N chemical shifts	30	30	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	150	148	98.7
¹³C chemical shifts	94	70	74.5
¹⁵N chemical shifts	4	4	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	15	15	100.0
¹³C chemical shifts	15	15	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	24	22	91.7
¹³C chemical shifts	24	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 33, Sequence coverage: 100.0%
- Total number of restraints: 1333
- Weight of restraints: 1.0 (1333)
- Potential type of restraints: square-well-parabolic (1333)
- Range of distance target values: 2.25, 5.8 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 33, Sequence coverage: 45.5%
  - Total number of restraints: 22
  - Weight of restraints: 1.0 (22)
  - Potential type of restraints: square-well-parabolic (22)
  - Range of distance target values: 2.0, 2.9 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 33, Sequence coverage: 66.7%
- Total number of restraints: 34
- Total number of restraints per polymer type: 34
- Weight of restraints: 1.0 (34)
- Potential type of restraints: square-well-parabolic (34)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords C2H2-type, NDP52, ubiquitin-binding, zinc finger

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Found 1 Document (2.237 seconds)

BMRB: 25423

Sample #1

Sample #2

Sample #3

Related entities 1. NDP52 ubiquitin-binding zinc finger, entity 1, : 2 : 2 : 17 entities Detail

Interaction partners 1. NDP52 ubiquitin-binding zinc finger, entity 1, : 149 interactors Detail

Experiments performed 7 experiments Detail

Instrument

Sample

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Sample

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NMR combined restraints 5 contents Detail