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BMRB: 16507

2KOH

NMR structure of mouse Par3-PDZ3 in complex with VE-Cadherin C-terminus

Authors

Volkman, B.F., Tyler, R.C., Peterson, F.C.

Assembly

MmPar3 PDZ3, MmVE-Cadherin

Entity

1. MmPar3 PDZ3 (polymer, Thiol state: all free), 111 monomers, 11888.28 Da Detail

GSDGTREFLT FEVPLNDSGS AGLGVSVKGN RSKENHADLG IFVKSIINGG AASKDGRLRV NDQLIAVNGE SLLGKANQEA METLRRSMST EGNKRGMIQL IVARRISRCN E

2. MmVE-Cadherin (polymer, Thiol state: not present), 16 monomers, 1821.053 Da Detail

MLAELYGSDP QEELII

Total weight

13709.333 Da

Max. entity weight

11888.28 Da

Source organism

Mus musculus

Exptl. method

solution NMR

Refine. method

AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT AND ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.4 %, Completeness: 93.7 %, Completeness (bb): 95.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.7 % (1323 of 1412)	93.5 % (690 of 738)	93.5 % (501 of 536)	95.7 % (132 of 138)
Backbone	95.5 % (724 of 758)	94.8 % (253 of 267)	95.6 % (350 of 366)	96.8 % (121 of 125)
Sidechain	92.4 % (708 of 766)	92.8 % (437 of 471)	92.2 % (260 of 282)	84.6 % (11 of 13)
Aromatic	71.4 % (30 of 42)	90.5 % (19 of 21)	52.4 % (11 of 21)
Methyl	97.2 % (138 of 142)	97.2 % (69 of 71)	97.2 % (69 of 71)

1. MmPar3 PDZ3

GSDGTREFLT FEVPLNDSGS AGLGVSVKGN RSKENHADLG IFVKSIINGG AASKDGRLRV NDQLIAVNGE SLLGKANQEA METLRRSMST EGNKRGMIQL IVARRISRCN E

2. MmVE-Cadherin

MLAELYGSDP QEELII

Show sample condition

Sample #1

Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 1.0 mM mPar3 PDZ3 (581-689) U-15N/13C, 2.0 mM VE-Cadherin (769-784), 20 mM sodium phosphate, 50 mM sodium chloride

#	Name	Isotope labeling	Concentration
1	MmPar3 PDZ3	[U-100% 13C; U-100% 15N]	1 mM
2	MmVE-Cadherin	natural abundance	2 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM
5	D2O	natural abundance	10 %
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	90 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 1.0 mM VE-Cadherin (769-784) U-15N/13C, 1.0 mM mPar3 PDZ3 (581-689), 20 mM sodium phosphate, 50 mM sodium chloride

#	Name	Isotope labeling	Concentration
8	MmVE-Cadherin	[U-100% 13C; U-100% 15N]	1 mM
9	MmPar3 PDZ3	natural abundance	1 mM
10	sodium phosphate	natural abundance	20 mM
11	sodium chloride	natural abundance	50 mM
12	D2O	natural abundance	10 %
13	sodium chloride	natural abundance	0.02 %
14	H2O	natural abundance	90 %

Protein Blocks Logo

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

Release date

2010-01-27

Citation

Distal interactions within the par3-VE-cadherin complex
Tyler, R.C., Peterson, F.C., Volkman, B.F.
Biochemistry (2010), 49, 951-957, PubMed 20047332 , DOI 10.1021/bi9017335 , Abstract

Entries sharing articles Swiss-Prot: 2 entries Detail

  Swiss-Prot: Q99NH2 released on 2003-05-16
    Title PARD3_MOUSE Entity Partitioning defective 3 homolog
  Swiss-Prot: P55284 released on 1996-10-01
    Title CADH5_MOUSE Entity Cadherin-5

Related entities 1. MmPar3 PDZ3, : 4 : 137 entities Detail

Related entities 2. MmVE-Cadherin, : 1 : 3 : 5 entities Detail

Interaction partners 1. MmPar3 PDZ3, : 10 : 1 interactors Detail

More details for 11 interactors identified by 8 citations

Interaction partners 2. MmVE-Cadherin, : 11 : 1 interactors Detail

More details for 12 interactors identified by 5 citations

Experiments performed 8 experiments Detail

1 3D_15N-separated_NOESY

Instrument

Bruker Avance II - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 1.0 mM mPar3 PDZ3 (581-689) U-15N/13C, 2.0 mM VE-Cadherin (769-784), 20 mM sodium phosphate, 50 mM sodium chloride

#	Name	Isotope labeling	Concentration
1	MmPar3 PDZ3	[U-100% 13C; U-100% 15N]	1 mM
2	MmVE-Cadherin	natural abundance	2 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM
5	D2O	natural abundance	10 %
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	90 %

2 3D_13C-separated_NOESY

Instrument

Bruker Avance II - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MmPar3 PDZ3	[U-100% 13C; U-100% 15N]	1 mM
2	MmVE-Cadherin	natural abundance	2 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM
5	D2O	natural abundance	10 %
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	90 %

3 3D_13C-separated_NOESY (AROMATIC)

Instrument

Bruker Avance II - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MmPar3 PDZ3	[U-100% 13C; U-100% 15N]	1 mM
2	MmVE-Cadherin	natural abundance	2 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM
5	D2O	natural abundance	10 %
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	90 %

4 3D_15N-separated_NOESY

Instrument

Bruker Avance II - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 1.0 mM VE-Cadherin (769-784) U-15N/13C, 1.0 mM mPar3 PDZ3 (581-689), 20 mM sodium phosphate, 50 mM sodium chloride

#	Name	Isotope labeling	Concentration
8	MmVE-Cadherin	[U-100% 13C; U-100% 15N]	1 mM
9	MmPar3 PDZ3	natural abundance	1 mM
10	sodium phosphate	natural abundance	20 mM
11	sodium chloride	natural abundance	50 mM
12	D2O	natural abundance	10 %
13	sodium chloride	natural abundance	0.02 %
14	H2O	natural abundance	90 %

5 3D_13C-separated_NOESY

Instrument

Bruker Avance II - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
8	MmVE-Cadherin	[U-100% 13C; U-100% 15N]	1 mM
9	MmPar3 PDZ3	natural abundance	1 mM
10	sodium phosphate	natural abundance	20 mM
11	sodium chloride	natural abundance	50 mM
12	D2O	natural abundance	10 %
13	sodium chloride	natural abundance	0.02 %
14	H2O	natural abundance	90 %

6 3D_13C-separated_NOESY (AROMATIC)

Instrument

Bruker Avance II - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
8	MmVE-Cadherin	[U-100% 13C; U-100% 15N]	1 mM
9	MmPar3 PDZ3	natural abundance	1 mM
10	sodium phosphate	natural abundance	20 mM
11	sodium chloride	natural abundance	50 mM
12	D2O	natural abundance	10 %
13	sodium chloride	natural abundance	0.02 %
14	H2O	natural abundance	90 %

7 3D_13C-F1-filtered_13C-F3-separated_NOESY

Instrument

Bruker Avance II - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
8	MmVE-Cadherin	[U-100% 13C; U-100% 15N]	1 mM
9	MmPar3 PDZ3	natural abundance	1 mM
10	sodium phosphate	natural abundance	20 mM
11	sodium chloride	natural abundance	50 mM
12	D2O	natural abundance	10 %
13	sodium chloride	natural abundance	0.02 %
14	H2O	natural abundance	90 %

8 3D_13C-F1-filtered_13C-F3-separated_NOESY

Instrument

Bruker Avance II - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MmPar3 PDZ3	[U-100% 13C; U-100% 15N]	1 mM
2	MmVE-Cadherin	natural abundance	2 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM
5	D2O	natural abundance	10 %
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	90 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16507_2koh.nef
Input source #2: Coordindates	2koh.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

-580-----590-------600-------610-------620-------630-------640-------650-------660-------670-------6
GSDGTREFLTFEVPLNDSGSAGLGVSVKGNRSKENHADLGIFVKSIINGGAASKDGRLRVNDQLIAVNGESLLGKANQEAMETLRRSMSTEGNKRGMIQL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSDGTREFLTFEVPLNDSGSAGLGVSVKGNRSKENHADLGIFVKSIINGGAASKDGRLRVNDQLIAVNGESLLGKANQEAMETLRRSMSTEGNKRGMIQL
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

80---------
IVARRISRCNE
|||||||||||
IVARRISRCNE
-------110-

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

-770-----780----
MLAELYGSDPQEELII
||||||||||||||||
MLAELYGSDPQEELII
--------10------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	111	0	0	100.0
B	B	16	0	0	100.0

Content subtype: combined_16507_2koh.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1333		99.1 (chain: A, length: 111), 93.8 (chain: B, length: 16)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	2622 (1)	noe	95.5 (chain: A, length: 111), 93.8 (chain: B, length: 16)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	115 (115)	.	65.8 (chain: A, length: 111), 31.2 (chain: B, length: 16)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 111, Sequence coverage: 99.1%
  - Entity_assembly_ID: B, Chain length: 16, Sequence coverage: 93.8%
- Total number of assignments
  - ¹H chemical shifts: 697
  - ¹⁵N chemical shifts: 137
  - ¹³C chemical shifts: 499
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- 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
  - Chain_ID: B

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	641	613	95.6
¹⁵N chemical shifts	132	124	93.9
¹³C chemical shifts	462	437	94.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	235	227	96.6
¹⁵N chemical shifts	110	107	97.3
¹³C chemical shifts	222	213	95.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	406	386	95.1
¹⁵N chemical shifts	22	17	77.3
¹³C chemical shifts	240	224	93.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	63	62	98.4
¹³C chemical shifts	63	62	98.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	17	15	88.2
¹³C chemical shifts	17	9	52.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	97	84	86.6
¹⁵N chemical shifts	16	13	81.2
¹³C chemical shifts	74	62	83.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	32	29	90.6
¹⁵N chemical shifts	15	13	86.7
¹³C chemical shifts	32	28	87.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	65	55	84.6
¹⁵N chemical shifts	1	0	0.0
¹³C chemical shifts	42	34	81.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	12	10	83.3
¹³C chemical shifts	12	10	83.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	4	4	100.0
¹³C chemical shifts	4	2	50.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 111, Sequence coverage: 95.5%
  - Entity_assembly_ID: B, Chain length: 16, Sequence coverage: 93.8%
- Total number of restraints: 2622
- Weight of restraints: 1.0 (2622)
- Potential type of restraints: upper-bound-parabolic (2622)
- Range of distance target values: 2.14, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 111, Sequence coverage: 65.8%
  - Entity_assembly_ID: B, Chain length: 16, Sequence coverage: 31.2%
- Total number of restraints: 115
- Total number of restraints per polymer type: 115
- Weight of restraints: 1.0 (115)
- Potential type of restraints: square-well-parabolic (115)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Par3, PDZ domain, VE Cadherin

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Found 1 Document (3.175 seconds)

BMRB: 16507

Sample #1

Sample #2

Entries sharing articles Swiss-Prot: 2 entries Detail

Related entities 1. MmPar3 PDZ3, : 4 : 137 entities Detail

Related entities 2. MmVE-Cadherin, : 1 : 3 : 5 entities Detail

Interaction partners 1. MmPar3 PDZ3, : 10 : 1 interactors Detail

Interaction partners 2. MmVE-Cadherin, : 11 : 1 interactors Detail

Experiments performed 8 experiments Detail

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NMR combined restraints 4 contents Detail