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Found 1 Document (0.92 seconds)

BMRB: 19302

2M9M

Solution Structure of ERCC4 domain of human FAAP24

Authors

Wu, F., Han, X., Shi, C., Gong, W., Tian, C.

Assembly

ERCC4 domain of human FAAP24

Entity

1. ERCC4 domain of human FAAP24 (polymer), 147 monomers, 16727.12 Da Detail

MEKNPPDDTG PVHVPLGHIV ANEKWRGSQL AQEMQGKIKL IFEDGLTPDF YLSNRCCILY VTEADLVAGN GYRKRLVRVR NSNNLKGIVV VEKTRMSEQY FPALQKFTVL DLGMVLLPVA SQMEASCLVI QLVQEQTKEL EHHHHHH

Formula weight

16727.12 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.6 %, Completeness: 81.7 %, Completeness (bb): 93.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	81.7 % (1428 of 1747)	80.2 % (731 of 911)	82.9 % (563 of 679)	85.4 % (134 of 157)
Backbone	93.8 % (814 of 868)	92.9 % (275 of 296)	94.2 % (407 of 432)	94.3 % (132 of 140)
Sidechain	72.8 % (740 of 1017)	73.8 % (454 of 615)	73.8 % (284 of 385)	11.8 % (2 of 17)
Aromatic	18.1 % (21 of 116)	34.5 % (20 of 58)	0.0 % (0 of 57)	100.0 % (1 of 1)
Methyl	93.8 % (167 of 178)	94.4 % (84 of 89)	93.3 % (83 of 89)

1. FAAP24-ERCC4

MEKNPPDDTG PVHVPLGHIV ANEKWRGSQL AQEMQGKIKL IFEDGLTPDF YLSNRCCILY VTEADLVAGN GYRKRLVRVR NSNNLKGIVV VEKTRMSEQY FPALQKFTVL DLGMVLLPVA SQMEASCLVI QLVQEQTKEL EHHHHHH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	FAAP24-ERCC4	[U-100% 13C; U-100% 15N]	0.5 ~ 0.8 mM
2	potassium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	50 mM
4	beta-mercaptoethanol	natural abundance	1 mM
5	EDTA	natural abundance	0.5 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
8	FAAP24-ERCC4	[U-100% 13C; U-100% 15N]	0.5 ~ 0.8 mM
9	potassium phosphate	natural abundance	50 mM
10	sodium chloride	natural abundance	50 mM
11	beta-mercaptoethanol	natural abundance	1 mM
12	EDTA	natural abundance	0.5 mM
13	D2O	natural abundance	100 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.18 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.18 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.13 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.09 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2M9M, Strand ID: A Detail

Release date

2013-09-15

Citation

Structure analysis of FAAP24 reveals single-stranded DNA-binding activity and domain functions in DNA damage response
Wang, Y., Han, X., Wu, F., Leung, J.W., Lowery, M.G., Do, H., Chen, J., Shi, C., Tian, C., Li, L., Gong, W.
Cell Res. (2013), 23, 1215-1228, PubMed 23999858 , DOI 10.1038/cr.2013.124 , Abstract

Related entities 1. ERCC4 domain of human FAAP24, : 1 : 2 : 7 entities Detail

Interaction partners 1. ERCC4 domain of human FAAP24, : 8 interactors Detail

More details for 8 interactors identified by 5 citations

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	FAAP24-ERCC4	[U-100% 13C; U-100% 15N]	0.5 ~ 0.8 mM
2	potassium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	50 mM
4	beta-mercaptoethanol	natural abundance	1 mM
5	EDTA	natural abundance	0.5 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

2 3D CBCA(CO)NH

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	FAAP24-ERCC4	[U-100% 13C; U-100% 15N]	0.5 ~ 0.8 mM
2	potassium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	50 mM
4	beta-mercaptoethanol	natural abundance	1 mM
5	EDTA	natural abundance	0.5 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

3 3D HNCACB

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	FAAP24-ERCC4	[U-100% 13C; U-100% 15N]	0.5 ~ 0.8 mM
2	potassium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	50 mM
4	beta-mercaptoethanol	natural abundance	1 mM
5	EDTA	natural abundance	0.5 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

4 3D HNCA

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	FAAP24-ERCC4	[U-100% 13C; U-100% 15N]	0.5 ~ 0.8 mM
2	potassium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	50 mM
4	beta-mercaptoethanol	natural abundance	1 mM
5	EDTA	natural abundance	0.5 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

5 3D HN(CO)CA

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	FAAP24-ERCC4	[U-100% 13C; U-100% 15N]	0.5 ~ 0.8 mM
2	potassium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	50 mM
4	beta-mercaptoethanol	natural abundance	1 mM
5	EDTA	natural abundance	0.5 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

6 3D HNCO

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	FAAP24-ERCC4	[U-100% 13C; U-100% 15N]	0.5 ~ 0.8 mM
2	potassium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	50 mM
4	beta-mercaptoethanol	natural abundance	1 mM
5	EDTA	natural abundance	0.5 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

7 3D HBHA(CO)NH

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	FAAP24-ERCC4	[U-100% 13C; U-100% 15N]	0.5 ~ 0.8 mM
2	potassium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	50 mM
4	beta-mercaptoethanol	natural abundance	1 mM
5	EDTA	natural abundance	0.5 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

8 3D H(CCO)NH

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	FAAP24-ERCC4	[U-100% 13C; U-100% 15N]	0.5 ~ 0.8 mM
2	potassium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	50 mM
4	beta-mercaptoethanol	natural abundance	1 mM
5	EDTA	natural abundance	0.5 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

9 3D C(CO)NH

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	FAAP24-ERCC4	[U-100% 13C; U-100% 15N]	0.5 ~ 0.8 mM
2	potassium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	50 mM
4	beta-mercaptoethanol	natural abundance	1 mM
5	EDTA	natural abundance	0.5 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

10 3D HCCH-TOCSY

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
8	FAAP24-ERCC4	[U-100% 13C; U-100% 15N]	0.5 ~ 0.8 mM
9	potassium phosphate	natural abundance	50 mM
10	sodium chloride	natural abundance	50 mM
11	beta-mercaptoethanol	natural abundance	1 mM
12	EDTA	natural abundance	0.5 mM
13	D2O	natural abundance	100 %

11 3D HCCH-COSY

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
8	FAAP24-ERCC4	[U-100% 13C; U-100% 15N]	0.5 ~ 0.8 mM
9	potassium phosphate	natural abundance	50 mM
10	sodium chloride	natural abundance	50 mM
11	beta-mercaptoethanol	natural abundance	1 mM
12	EDTA	natural abundance	0.5 mM
13	D2O	natural abundance	100 %

12 3D 1H-15N NOESY

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	FAAP24-ERCC4	[U-100% 13C; U-100% 15N]	0.5 ~ 0.8 mM
2	potassium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	50 mM
4	beta-mercaptoethanol	natural abundance	1 mM
5	EDTA	natural abundance	0.5 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

13 3D 1H-13C NOESY

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
8	FAAP24-ERCC4	[U-100% 13C; U-100% 15N]	0.5 ~ 0.8 mM
9	potassium phosphate	natural abundance	50 mM
10	sodium chloride	natural abundance	50 mM
11	beta-mercaptoethanol	natural abundance	1 mM
12	EDTA	natural abundance	0.5 mM
13	D2O	natural abundance	100 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19302_2m9m.nef
Input source #2: Coordindates	2m9m.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	None
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)

None

Non-standard residues

None

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MEKNPPDDTGPVHVPLGHIVANEKWRGSQLAQEMQGKIKLIFEDGLTPDFYLSNRCCILYVTEADLVAGNGYRKRLVRVRNSNNLKGIVVVEKTRMSEQY
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MEKNPPDDTGPVHVPLGHIVANEKWRGSQLAQEMQGKIKLIFEDGLTPDFYLSNRCCILYVTEADLVAGNGYRKRLVRVRNSNNLKGIVVVEKTRMSEQY

-------110-------120-------130-------140-------
FPALQKFTVLDLGMVLLPVASQMEASCLVIQLVQEQTKELEHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||
FPALQKFTVLDLGMVLLPVASQMEASCLVIQLVQEQTKELEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	147	0	0	100.0

Content subtype: combined_19302_2m9m.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1380		93.9 (chain: A, length: 147)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2252 (1)	noe	90.5 (chain: A, length: 147)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 147, Sequence coverage: 93.9%
- Total number of assignments
  - ¹H chemical shifts: 707
  - ¹³C chemical shifts: 542
  - ¹⁵N chemical shifts: 131
- 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	911	707	77.6
¹³C chemical shifts	679	542	79.8
¹⁵N chemical shifts	164	131	79.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	296	274	92.6
¹³C chemical shifts	294	274	93.2
¹⁵N chemical shifts	140	130	92.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	615	433	70.4
¹³C chemical shifts	385	268	69.6
¹⁵N chemical shifts	24	1	4.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	94	80	85.1
¹³C chemical shifts	94	79	84.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	58	20	34.5
¹³C chemical shifts	57	0	0.0
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 147, Sequence coverage: 90.5%
- Total number of restraints: 2251
- Weight of restraints: 1.0 (2251)
- Potential type of restraints: square-well-parabolic (2251)
- Range of distance target values: 2.3, 3.9 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords ERCC4 domain, FAAP24, Fanconi anemia, Solution NMR

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Found 1 Document (0.92 seconds)

BMRB: 19302

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. ERCC4 domain of human FAAP24, : 1 : 2 : 7 entities Detail

Interaction partners 1. ERCC4 domain of human FAAP24, : 8 interactors Detail

Experiments performed 13 experiments Detail

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NMR combined restraints 3 contents Detail