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Found 1 Document (3.617 seconds)

BMRB: 30659

6U4N

Solution structure of paxillin LIM4 in complex with kindlin-2 F0

Authors

Zhu, L., Qin, J.

Assembly

Fermitin family homolog 2, Paxillin

Entity

1. Fermitin family homolog 2, Paxillin, entity 1 (polymer, Thiol state: free and other bound), 112 monomers, 12981.86 Da Detail

GAMDPEFMAL DGIRMPDGCY ADGTWELSVH VTDLNRDVTL RVTGEVHIGG VMLKLVEKLD VKKDWSDHAL WWEKKRTWLL KTHWTLDKYG IQADAKLQFT PQHKLLRLQL PN

2. Fermitin family homolog 2, Paxillin, entity 2 (polymer, Thiol state: free and other bound), 72 monomers, 8295.643 Da Detail

GAMDPEFYHE RRGSLCSGCQ KPITGRCITA MAKKFHPEHF VCAFCLKQLN KGTFKEQNDK PYCQNCFLKL FC

3. Fermitin family homolog 2, Paxillin, entity ZN (non-polymer), 65.409 × 2 Da

Total weight

21408.322 Da

Max. entity weight

12981.86 Da

Entity Connection

na 8 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	2:CYS16:SG	3:ZN1:ZN
2	na	sing	2:CYS19:SG	3:ZN1:ZN
3	na	sing	2:HIS36:ND1	3:ZN1:ZN
4	na	sing	2:HIS39:ND1	3:ZN1:ZN
5	na	sing	2:CYS42:SG	3:ZN1:ZN
6	na	sing	2:CYS45:SG	3:ZN1:ZN
7	na	sing	2:CYS63:SG	3:ZN1:ZN
8	na	sing	2:CYS66:SG	3:ZN1:ZN

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 90.8 %, Completeness: 67.7 %, Completeness (bb): 71.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	67.7 % (1506 of 2226)	71.9 % (836 of 1163)	59.3 % (515 of 868)	79.5 % (155 of 195)
Backbone	71.9 % (782 of 1088)	84.2 % (314 of 373)	60.9 % (328 of 539)	79.5 % (140 of 176)
Sidechain	67.0 % (877 of 1309)	66.1 % (522 of 790)	68.0 % (340 of 500)	78.9 % (15 of 19)
Aromatic	9.7 % (22 of 226)	11.5 % (13 of 113)	3.7 % (4 of 107)	83.3 % (5 of 6)
Methyl	87.4 % (159 of 182)	86.8 % (79 of 91)	87.9 % (80 of 91)

1. entity 1

GAMDPEFMAL DGIRMPDGCY ADGTWELSVH VTDLNRDVTL RVTGEVHIGG VMLKLVEKLD VKKDWSDHAL WWEKKRTWLL KTHWTLDKYG IQADAKLQFT PQHKLLRLQL PN

2. entity 2

GAMDPEFYHE RRGSLCSGCQ KPITGRCITA MAKKFHPEHF VCAFCLKQLN KGTFKEQNDK PYCQNCFLKL FC

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 Pa, Temperature 298 K, pH 6.8, Details 0.55 mM U-15N, U-13C paxillin LIM4, 0.89 mM kindlin-2 F0, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	paxillin LIM4	[U-15N; U-13C]	0.55 mM
2	kindlin-2 F0	natural abundance	0.89 mM
3	NaCl	natural abundance	50 mM

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 Pa, Temperature 298 K, pH 6.8, Details 0.54 mM U-15N, U-13C kindlin-2 F0, 0.85 mM paxillin LIM4, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
4	paxillin LIM4	natural abundance	0.85 mM
5	kindlin-2 F0	U-15N, U-13C	0.54 mM
6	NaCl	natural abundance	50 mM

Sample #3

Solvent system 99.8% D2O, Pressure 1 Pa, Temperature 298 K, pH 6.8, Details 0.55 mM U-15N, U-13C paxillin LIM4, 0.89 mM kindlin-2 F0, 99.8% D2O

#	Name	Isotope labeling	Concentration
7	paxillin LIM4	U-15N, U-13C	0.55 mM
8	kindlin-2 F0	natural abundance	0.89 mM
9	NaCl	natural abundance	50 mM

Sample #4

Solvent system 99.8% D2O, Pressure 1 Pa, Temperature 298 K, pH 6.8, Details 0.54 mM U-15N, U-13C kindlin-2 F0, 0.85 mM paxillin LIM4, 99.8% D2O

#	Name	Isotope labeling	Concentration
10	paxillin LIM4	natural abundance	0.85 mM
11	kindlin-2 F0	U-15N, U-13C	0.54 mM
12	NaCl	natural abundance	50 mM

LACS Plot; CA

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

Referencing offset: 0.41 ppm, Outliers: 4 Detail

LACS Plot; CB

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

Referencing offset: 0.41 ppm, Outliers: 4 Detail

LACS Plot; HA

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

Referencing offset: 0.14 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 6U4N, Strand ID: A, B Detail

Release date

2019-09-12

Citation

Structural Basis of Paxillin Recruitment by Kindlin-2 in Regulating Cell Adhesion
Zhu, L., Liu, H., Lu, F., Yang, J., Byzova, T.V., Qin, J.
Structure (2019), 27, 1686-1697, PubMed 31590942 , DOI 10.1016/j.str.2019.09.006 , Abstract

Related entities 1. Fermitin family homolog 2, Paxillin, entity 1, : 1 : 7 : 25 entities Detail

Related entities 2. Fermitin family homolog 2, Paxillin, entity 2, : 4 : 263 entities Detail

Interaction partners 1. Fermitin family homolog 2, Paxillin, entity 1, : 14 interactors Detail

More details for 14 interactors identified by 7 citations

Interaction partners 2. Fermitin family homolog 2, Paxillin, entity 2, : 57 interactors Detail

More details for 57 interactors identified by 30 citations

Experiments performed 4 experiments Detail

Chemical shift validation 5 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30659_3.str
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)
2:16:CYS:SG	3:1:ZN:ZN	reduced, CA 57.282, CB 31.458 ppm	unknown	n/a
2:19:CYS:SG	3:1:ZN:ZN	reduced, CA 58.186, CB 31.506 ppm	unknown	n/a
2:36:HIS:ND1	3:1:ZN:ZN	unknown	unknown	n/a
2:39:HIS:ND1	3:1:ZN:ZN	unknown	unknown	n/a
2:42:CYS:SG	4:1:ZN:ZN	reduced, CA 59.236, CB 30.925 ppm	unknown	n/a
2:45:CYS:SG	4:1:ZN:ZN	oxidized 6.8%, reduced 93.2%, CA 59.552, CB 32.145 ppm	unknown	n/a
2:63:CYS:SG	4:1:ZN:ZN	reduced, CA 57.383, CB 30.749 ppm	unknown	n/a
2:66:CYS:SG	4:1:ZN:ZN	reduced, CA 65.037, CB 29.266 ppm	unknown	n/a

Non-standard residues

None

Content subtype: bmr30659_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1641		83.9 (chain: 1, length: 112), 98.6 (chain: 2, length: 72)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 112, Sequence coverage: 83.9%
  - Entity_assembly_ID: 2, Chain length: 72, Sequence coverage: 98.6%
- Total number of assignments
  - ¹H chemical shifts: 985
  - ¹³C chemical shifts: 506
  - ¹⁵N chemical shifts: 150
- Completeness of assignments
  - Entity_assemble_ID: 1
  - Entity_assemble_ID: 2
- 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: 1
  - Chain_ID: 2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	702	459	65.4
¹³C chemical shifts	532	295	55.5
¹⁵N chemical shifts	125	85	68.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	228	176	77.2
¹³C chemical shifts	224	94	42.0
¹⁵N chemical shifts	108	77	71.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	474	283	59.7
¹³C chemical shifts	308	201	65.3
¹⁵N chemical shifts	17	8	47.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	72	58	80.6
¹³C chemical shifts	72	58	80.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	64	7	10.9
¹³C chemical shifts	58	0	0.0
¹⁵N chemical shifts	6	5	83.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	461	364	79.0
¹³C chemical shifts	336	211	62.8
¹⁵N chemical shifts	78	65	83.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	145	132	91.0
¹³C chemical shifts	144	71	49.3
¹⁵N chemical shifts	68	58	85.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	316	232	73.4
¹³C chemical shifts	192	140	72.9
¹⁵N chemical shifts	10	7	70.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	25	23	92.0
¹³C chemical shifts	25	23	92.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	49	0	0.0
¹³C chemical shifts	49	0	0.0

Keywords CELL ADHESION, Complex, LIM domain, Ubiquitin fold, Zinc finger

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Found 1 Document (3.617 seconds)

BMRB: 30659

Sample #1

Sample #2

Sample #3

Sample #4

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Fermitin family homolog 2, Paxillin, entity 1, : 1 : 7 : 25 entities Detail

Related entities 2. Fermitin family homolog 2, Paxillin, entity 2, : 4 : 263 entities Detail

Interaction partners 1. Fermitin family homolog 2, Paxillin, entity 1, : 14 interactors Detail

Interaction partners 2. Fermitin family homolog 2, Paxillin, entity 2, : 57 interactors Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 5 contents Detail