BMRBj - BMREntryMaster

Found 1 Document (6.971 seconds)

BMRB: 25176

2MTP

The structure of Filamin repeat 21 bound to integrin

Authors

Liu, J., Qin, J.

Assembly

Filamin repeat 21 bound to integrin

Entity

1. Filamin repeat 21 bound to integrin, entity 1 (polymer), 95 monomers, 9752.635 Da Detail

GGAHKVRAGG PGLERAEAGV PAEFSIWTRE AGAGGLAIAV EGPSKAEISF EDRKDGSCGV AYVVQEPGDY EVSVKFNEEH IPDSPFVVPV ASPSG

2. Filamin repeat 21 bound to integrin, entity 2 (polymer, Thiol state: not present), 21 monomers, 2577.756 Da Detail

WKVGFFKRNR PPLEEDDEEG E

3. Filamin repeat 21 bound to integrin, entity 3 (polymer, Thiol state: not present), 47 monomers, 5606.220 Da Detail

KKKITIHDRK EFAKFEEERA RAKWDTANNP LYKEATSTFT NITYRGT

Total weight

17936.611 Da

Max. entity weight

9752.635 Da

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: 70.3 %, Completeness (bb): 76.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	70.3 % (1299 of 1848)	78.7 % (759 of 965)	56.4 % (407 of 722)	82.6 % (133 of 161)
Backbone	76.4 % (730 of 956)	96.7 % (321 of 332)	58.5 % (276 of 472)	87.5 % (133 of 152)
Sidechain	67.1 % (696 of 1038)	69.2 % (438 of 633)	65.2 % (258 of 396)	0.0 % (0 of 9)
Aromatic	19.4 % (33 of 170)	37.6 % (32 of 85)	1.2 % (1 of 82)	0.0 % (0 of 3)
Methyl	93.0 % (132 of 142)	95.8 % (68 of 71)	90.1 % (64 of 71)

1. entity 1

GGAHKVRAGG PGLERAEAGV PAEFSIWTRE AGAGGLAIAV EGPSKAEISF EDRKDGSCGV AYVVQEPGDY EVSVKFNEEH IPDSPFVVPV ASPSG

2. entity 2

WKVGFFKRNR PPLEEDDEEG E

3. entity 3

KKKITIHDRK EFAKFEEERA RAKWDTANNP LYKEATSTFT NITYRGT

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N; U-80% 2H]	1 mM
2	entity_2	[U-100% 13C; U-100% 15N; U-80% 2H]	0.0 ~ 0.0 mM
3	entity_3	[U-100% 13C; U-100% 15N; U-80% 2H]	0.0 ~ 0.0 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

LACS Plot; CA

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

Referencing offset: -0.17 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.17 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: -0.04 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2015-03-19

Citation

Structural mechanism of integrin inactivation by filamin
Liu, J., Das, M., Yang, J., Ithychanda, S.S., Yakubenko, V.P., Plow, E.F., Qin, J.
Nat. Struct. Mol. Biol. (2015), 22, 383-389, PubMed 25849143 , DOI 10.1038/nsmb.2999 , Abstract

Related entities 1. Filamin repeat 21 bound to integrin, entity 1, : 1 : 4 : 10 : 471 entities Detail

Related entities 2. Filamin repeat 21 bound to integrin, entity 2, : 1 : 7 : 4 : 11 entities Detail

Related entities 3. Filamin repeat 21 bound to integrin, entity 3, : 1 : 13 : 62 entities Detail

Interaction partners 1. Filamin repeat 21 bound to integrin, entity 1, : 142 : 1 interactors Detail

More details for 143 interactors identified by 56 citations

Interaction partners 2. Filamin repeat 21 bound to integrin, entity 2, : 2 : 1 interactors Detail

More details for 3 interactors identified by 3 citations

Interaction partners 3. Filamin repeat 21 bound to integrin, entity 3, : 5 interactors Detail

More details for 5 interactors identified by 5 citations

Experiments performed 2 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25176_2mtp.nef
Input source #2: Coordindates	2mtp.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

----2240---2250------2260------2270------2280------2290------2300------2310------2320------2330
GGAHKVRAGGPGLERAEAGVPAEFSIWTREAGAGGLAIAVEGPSKAEISFEDRKDGSCGVAYVVQEPGDYEVSVKFNEEHIPDSPFVVPVASPSG
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GGAHKVRAGGPGLERAEAGVPAEFSIWTREAGAGGLAIAVEGPSKAEISFEDRKDGSCGVAYVVQEPGDYEVSVKFNEEHIPDSPFVVPVASPSG
--------10--------20--------30--------40--------50--------60--------70--------80--------90-----

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

--990----1000--------
WKVGFFKRNRPPLEEDDEEGE
|||||||||||||||||||||
WKVGFFKRNRPPLEEDDEEGE
--------10--------20-

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

--720-------730-------740-------750-------760--
KKKITIHDRKEFAKFEEERARAKWDTANNPLYKEATSTFTNITYRGT
|||||||||||||||||||||||||||||||||||||||||||||||
KKKITIHDRKEFAKFEEERARAKWDTANNPLYKEATSTFTNITYRGT
--------10--------20--------30--------40-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Sequence coverage (%)
A	A	95	100.0
B	B	21	100.0
C	C	47	100.0

Content subtype: combined_25176_2mtp.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1322		100.0 (chain: A, length: 95), 100.0 (chain: B, length: 21), 100.0 (chain: C, length: 47)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	812 (1)	noe	100.0 (chain: A, length: 95)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	617 (1)	noe	11.6 (chain: A, length: 95), 100.0 (chain: B, length: 21), 100.0 (chain: C, length: 47)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	124 (124)	.	88.4 (chain: A, length: 95)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 21, Sequence coverage: 100.0%
  - Entity_assembly_ID: C, Chain length: 47, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 789
  - ¹³C chemical shifts: 400
  - ¹⁵N chemical shifts: 133
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
  - Entity_assemble_ID: C
- 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
  - Chain_ID: B
  - Chain_ID: C

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2315	HIS	HE2	7.103

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	517	444	85.9
¹³C chemical shifts	397	263	66.2
¹⁵N chemical shifts	94	87	92.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	196	195	99.5
¹³C chemical shifts	190	95	50.0
¹⁵N chemical shifts	87	87	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	321	249	77.6
¹³C chemical shifts	207	168	81.2
¹⁵N chemical shifts	7	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	47	45	95.7
¹³C chemical shifts	47	45	95.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	38	13	34.2
¹³C chemical shifts	37	1	2.7
¹⁵N chemical shifts	1	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	142	108	76.1
¹³C chemical shifts	100	0	0.0
¹⁵N chemical shifts	23	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	42	40	95.2
¹³C chemical shifts	42	0	0.0
¹⁵N chemical shifts	19	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	100	68	68.0
¹³C chemical shifts	58	0	0.0
¹⁵N chemical shifts	4	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	4	4	100.0
¹³C chemical shifts	4	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	16	12	75.0
¹³C chemical shifts	15	0	0.0
¹⁵N chemical shifts	1	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	306	206	67.3
¹³C chemical shifts	225	137	60.9
¹⁵N chemical shifts	54	46	85.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	94	88	93.6
¹³C chemical shifts	94	47	50.0
¹⁵N chemical shifts	46	46	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	212	118	55.7
¹³C chemical shifts	131	90	68.7
¹⁵N chemical shifts	8	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	20	19	95.0
¹³C chemical shifts	20	19	95.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	31	5	16.1
¹³C chemical shifts	30	0	0.0
¹⁵N chemical shifts	1	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 100.0%
- Total number of restraints: 812
- Weight of restraints: 1.0 (812)
- Potential type of restraints: square-well-parabolic (812)
- Range of distance target values: 2.25, 4.4 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
  - Chain_ID: C
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 11.6%
    - Entity_assembly_ID: B, Chain length: 21, Sequence coverage: 100.0%
    - Entity_assembly_ID: C, Chain length: 47, Sequence coverage: 100.0%
  - Total number of restraints: 617
  - Weight of restraints: 1.0 (617)
  - Potential type of restraints: square-well-parabolic (617)
  - Range of distance target values: 2.1, 5.2 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
    - Chain_ID: C
  - 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: 95, Sequence coverage: 88.4%
- Total number of restraints: 124
- Total number of restraints per polymer type: 124
- Weight of restraints: 1.0 (124)
- Potential type of restraints: square-well-parabolic (124)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords integrin, filamin

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Found 1 Document (6.971 seconds)

BMRB: 25176

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Filamin repeat 21 bound to integrin, entity 1, : 1 : 4 : 10 : 471 entities Detail

Related entities 2. Filamin repeat 21 bound to integrin, entity 2, : 1 : 7 : 4 : 11 entities Detail

Related entities 3. Filamin repeat 21 bound to integrin, entity 3, : 1 : 13 : 62 entities Detail

Interaction partners 1. Filamin repeat 21 bound to integrin, entity 1, : 142 : 1 interactors Detail

Interaction partners 2. Filamin repeat 21 bound to integrin, entity 2, : 2 : 1 interactors Detail

Interaction partners 3. Filamin repeat 21 bound to integrin, entity 3, : 5 interactors Detail

Experiments performed 2 experiments Detail

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail