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BMRB: 25005

2MPX

THREE-DIMENSIONAL STRUCTURE OF CAP-GLY DOMAIN ASSEMBLED ON MICROTUBULES DETERMINED BY MAS NMR SPECTROSCOPY

Authors

Yan, S., Polenova, T., Williams, J.C., Hou, G., Zhang, H.

Assembly

CAP-GLY DOMAIN

Entity

1. CAP-Gly (polymer, Thiol state: all free), 89 monomers, 9512.475 Da Detail

STEASARPLR VGSRVEVIGK GHRGTVAYVG ATLFATGKWV GVILDEAKGK NDGTVQGRKY FTCDEGHGIF VRQSQIQVFE DGADTTSPE

2. Bovine Alpha Tubulin (polymer, Thiol state: all free), 451 monomers, 50053.85 Da Detail

MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHPE QLITGKEDAA NNYARGHYTI GKEIIDLVLD RIRKLADQCT GLQGFSVFHS FGGGTGSGFT SLLMERLSVD YGKKSKLEFS IYPAPQVSTA VVEPYNSILT THTTLEHSDC AFMVDNEAIY DICRRNLDIE RPTYTNLNRL IGQIVSSITA SLRFDGALNV DLTEFQTNLV PYPRGHFPLA TYAPVISAEK AYHEQLSVAE ITNACFEPAN QMVKCDPRHG KYMACCLLYR GDVVPKDVNA AIATIKTKRT IQFVDWCPTG FKVGINYEPP TVVPGGDLAK VQRAVCMLSN TTAIAEAWAR LDHKFDLMYA KRAFVHWYVG EGMEEGEFSE AREDMAALEK DYEEVGVDSV EGEGEEEGEE Y

3. Bovine Beta Tubulin (polymer, Thiol state: all free), 445 monomers, 49860.40 Da Detail

MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDNF VFGQSGAGNN WAKGHYTEGA ELVDSVLDVV RKESESCDCL QGFQLTHSLG GGTGSGMGTL LISKIREEYP DRIMNTFSVV PSPKVSDTVV EPYNATLSVH QLVENTDETY CIDNEALYDI CFRTLKLTTP TYGDLNHLVS ATMSGVTTCL RFPGQLNADL RKLAVNMVPF PRLHFFMPGF APLTSRGSQQ YRALTVPELT QQMFDAKNMM AACDPRHGRY LTVAAVFRGR MSMKEVDEQM LNVQNKNSSY FVEWIPNNVK TAVCDIPPRG LKMSATFIGN STAIQELFKR ISEQFTAMFR RKAFLHWYTG EGMDEMEFTE AESNMNDLVS EYQQYQDATA DEQGEFEEEG EEDEA

4. TAXOL (non-polymer), 853.906 Da
5. GUANOSINE-5'-TRIPHOSPHATE (non-polymer), 523.180 Da

Total weight

110803.81 Da

Max. entity weight

50053.85 Da

Source organism

Rattus norvegicus , Bos taurus

Exptl. method

NMR

Refine. method

simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 8.5 %, Completeness: 6.7 %, Completeness (bb): 7.9 % Detail

Polymer type: polypeptide(L)

	Total	¹³C	¹⁵N
All	6.7 % (364 of 5415)	6.4 % (281 of 4382)	8.0 % (83 of 1033)
Backbone	7.9 % (303 of 3812)	7.7 % (221 of 2869)	8.7 % (82 of 943)
Sidechain	5.1 % (128 of 2502)	5.3 % (127 of 2412)	1.1 % (1 of 90)
Aromatic	0.4 % (2 of 487)	0.4 % (2 of 478)	0.0 % (0 of 9)
Methyl	7.2 % (37 of 517)	7.2 % (37 of 517)

1. CAP-Gly

STEASARPLR VGSRVEVIGK GHRGTVAYVG ATLFATGKWV GVILDEAKGK NDGTVQGRKY FTCDEGHGIF VRQSQIQVFE DGADTTSPE

2. Bovine Alpha Tubulin

3. Bovine Beta Tubulin

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	na	indirect	0.2514495
¹⁵N	DSS	methyl protons	0.0 ppm	na	indirect	0.1013291

Referencing offset: 0.03 ppm, Outliers: 3 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	na	indirect	0.2514495
¹⁵N	DSS	methyl protons	0.0 ppm	na	indirect	0.1013291

Referencing offset: 0.03 ppm, Outliers: 3 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	na	indirect	0.2514495
¹⁵N	DSS	methyl protons	0.0 ppm	na	indirect	0.1013291

Referencing offset: -0.03 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2MPX, Strand ID: C Detail

Release date

2015-10-29

Citation

THREE-DIMENSIONAL STRUCTURE OF CAP-GLY DOMAIN ASSEMBLED ON MICROTUBULES DETERMINED BY MAS NMR SPECTROSCOPY
Yan, S., Polenova, T., Williams, J., Zhang, H., Hou, G., Ahmed, S.
Not known

Related entities 1. CAP-Gly, : 5 : 9 : 104 entities Detail

Related entities 2. Bovine Alpha Tubulin, : 7 : 19 : 437 entities Detail

Related entities 3. Bovine Beta Tubulin, : 26 : 1 : 27 : 400 entities Detail

Experiments performed 9 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25005_2mpx.nef
Input source #2: Coordindates	2mpx.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): C vs Auth_asym_ID (model): C

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
C	C	70	0	0	100.0

Content subtype: combined_25005_2mpx.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	312		100.0 (chain: C, length: 70)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2354 (1)	noe	100.0 (chain: C, length: 70)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	76 (1)	hbond	70.0 (chain: C, length: 70)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	112 (112)	.	100.0 (chain: C, length: 70)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: C, Chain length: 70, Sequence coverage: 100.0%
- Total number of assignments
  - ¹³C chemical shifts: 243
  - ¹⁵N chemical shifts: 69
- Completeness of assignments
  - Entity_assemble_ID: C
- 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: C

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
57	TRP	CG	111.66
63	ASP	CG	179.73
69	ASN	CG	178.5
70	ASP	CG	182.48
85	HIS	CG	132.61

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	308	238	77.3
¹⁵N chemical shifts	80	69	86.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	140	132	94.3
¹⁵N chemical shifts	69	69	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	168	106	63.1
¹⁵N chemical shifts	11	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	41	34	82.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	32	0	0.0
¹⁵N chemical shifts	1	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: C, Chain length: 70, Sequence coverage: 100.0%
- Total number of restraints: 2351
- Weight of restraints: 1.0 (2351)
- Potential type of restraints: square-well-parabolic (2351)
- Range of distance target values: 3.35, 4.6 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: C
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: C, Chain length: 70, Sequence coverage: 70.0%
  - Total number of restraints: 76
  - Weight of restraints: 1.0 (76)
  - Potential type of restraints: square-well-parabolic (76)
  - Range of distance target values: 1.9, 2.9 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - 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: C, Chain length: 70, Sequence coverage: 100.0%
- Total number of restraints: 112
- Total number of restraints per polymer type: 112
- Weight of restraints: 1.0 (112)
- Potential type of restraints: square-well-parabolic (112)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: C

Keywords structure of CAP-Gly domain assembled on microtubules

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Found 1 Document (1.126 seconds)

BMRB: 25005

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. CAP-Gly, : 5 : 9 : 104 entities Detail

Related entities 2. Bovine Alpha Tubulin, : 7 : 19 : 437 entities Detail

Related entities 3. Bovine Beta Tubulin, : 26 : 1 : 27 : 400 entities Detail

Interaction partners 1. CAP-Gly, : 4 interactors Detail

Interaction partners 2. Bovine Alpha Tubulin, : 4 : 1 interactors Detail

Interaction partners 3. Bovine Beta Tubulin, : 2 : 1 interactors Detail

Experiments performed 9 experiments Detail

Instrument

Instrument

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Instrument

Instrument

Instrument

Instrument

Instrument

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NMR combined restraints 5 contents Detail