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Found 1 Document (0.799 seconds)

BMRB: 19215

2M7W

Independently verified structure of gp41-M-MAT, a membrane associated MPER trimer from HIV-1 gp41

Authors

Martin, J.W., Reardon, P.N., Sage, H.S., Dennison, S.MOSES., Alam, S.MUNIR., Haynes, B.F., Spicer, L.D., Donald, B.R.

Assembly

gp41-M-MAT

Entity

1. gp41-M-MAT (polymer, Thiol state: not present), 59 monomers, 7005.765 × 3 Da Detail

GYIPEAPRDG QAYVRKDGEW VLLSTFLGSS GNEQELLELD KWASLWNWFN ITNWLWYIK

Total weight

21017.295 Da

Max. entity weight

7005.765 Da

Source organism

Human immunodeficiency virus 1

Exptl. method

solution NMR

Refine. method

complete search, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.9 %, Completeness: 64.7 %, Completeness (bb): 87.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	64.7 % (477 of 737)	63.8 % (243 of 381)	58.9 % (169 of 287)	94.2 % (65 of 69)
Backbone	87.4 % (306 of 350)	84.3 % (102 of 121)	86.0 % (148 of 172)	98.2 % (56 of 57)
Sidechain	50.1 % (221 of 441)	54.2 % (141 of 260)	42.0 % (71 of 169)	75.0 % (9 of 12)
Aromatic	10.3 % (12 of 116)	10.3 % (6 of 58)	0.0 % (0 of 52)	100.0 % (6 of 6)
Methyl	64.5 % (40 of 62)	83.9 % (26 of 31)	45.2 % (14 of 31)

1. gp41-M-MAT

GYIPEAPRDG QAYVRKDGEW VLLSTFLGSS GNEQELLELD KWASLWNWFN ITNWLWYIK

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	gp41-M-MAT	[U-99% 2H]	2 mM
2	sodium phosphate	natural abundance	50 mM
3	DPC	natural abundance	100 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
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: 0.24 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: 0.24 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: -0.06 ppm, Outliers: 2 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: -0.33 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 18 models in PDB: 2M7W, Strand ID: A, B, C Detail

Release date

2013-05-12

Citation

Structure of an HIV-1-neutralizing antibody target, the lipid-bound gp41 envelope membrane proximal region trimer
Reardon, P.N., Sage, H., Dennison, S., Martin, J.W., Donald, B.R., Alam, S., Haynes, B.F., Spicer, L.D.
Proc. Natl. Acad. Sci. U. S. A. (2014), 111, 1391-1396, PubMed 24474763 , DOI 10.1073/pnas.1309842111 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 18237 released on 2013-02-04
Title Structure of gp41-M-MAT, a membrane associated MPER trimer from HIV-1 gp41.

Related entities 1. gp41-M-MAT, : 1 : 1 : 3 entities Detail

Experiments performed 5 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_19215_2m7w.nef
Input source #2: Coordindates	2m7w.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---------
GYIPEAPRDGQAYVRKDGEWVLLSTFLGSSGNEQELLELDKWASLWNWFNITNWLWYIK
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GYIPEAPRDGQAYVRKDGEWVLLSTFLGSSGNEQELLELDKWASLWNWFNITNWLWYIK

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

--------10--------20--------30--------40--------50---------
GYIPEAPRDGQAYVRKDGEWVLLSTFLGSSGNEQELLELDKWASLWNWFNITNWLWYIK
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GYIPEAPRDGQAYVRKDGEWVLLSTFLGSSGNEQELLELDKWASLWNWFNITNWLWYIK

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

--------10--------20--------30--------40--------50---------
GYIPEAPRDGQAYVRKDGEWVLLSTFLGSSGNEQELLELDKWASLWNWFNITNWLWYIK
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GYIPEAPRDGQAYVRKDGEWVLLSTFLGSSGNEQELLELDKWASLWNWFNITNWLWYIK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Sequence coverage (%)
A	A	59	100.0
B	B	59	100.0
C	C	59	100.0

Content subtype: combined_19215_2m7w.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	439		93.2 (chain: A, length: 59)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1057 (1)	noe	91.5 (chain: A, length: 59), 91.5 (chain: B, length: 59), 91.5 (chain: C, length: 59)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	255 (255)	.	83.1 (chain: A, length: 59), 83.1 (chain: B, length: 59), 83.1 (chain: C, length: 59)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_3	OK	144 (144)	.	81.4 (chain: A, length: 59), 81.4 (chain: B, length: 59), 81.4 (chain: C, length: 59)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 59, Sequence coverage: 93.2%
- Total number of assignments
  - ¹H chemical shifts: 223
  - ¹³C chemical shifts: 152
  - ¹⁵N chemical shifts: 64
- Completeness of assignments
  - Entity_assemble_ID: A
- 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	381	223	58.5
¹³C chemical shifts	287	152	53.0
¹⁵N chemical shifts	71	64	90.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	121	100	82.6
¹³C chemical shifts	118	97	82.2
¹⁵N chemical shifts	57	55	96.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	260	123	47.3
¹³C chemical shifts	169	55	32.5
¹⁵N chemical shifts	14	9	64.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	31	23	74.2
¹³C chemical shifts	31	6	19.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	58	6	10.3
¹³C chemical shifts	52	0	0.0
¹⁵N chemical shifts	6	6	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: 59, Sequence coverage: 91.5%
  - Entity_assembly_ID: B, Chain length: 59, Sequence coverage: 91.5%
  - Entity_assembly_ID: C, Chain length: 59, Sequence coverage: 91.5%
- Total number of restraints: 1054
- Weight of restraints: 1.0 (1054)
- Potential type of restraints: square-well-parabolic (1054)
- Range of distance target values: 1.5, 3.25 (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_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 59, Sequence coverage: 83.1%
  - Entity_assembly_ID: B, Chain length: 59, Sequence coverage: 83.1%
  - Entity_assembly_ID: C, Chain length: 59, Sequence coverage: 83.1%
- Total number of restraints: 255
- Total number of restraints per polymer type: 255
- Weight of restraints: 1.0 (255)
- Potential type of restraints: square-well-parabolic (255)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_3

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 59, Sequence coverage: 81.4%

--------10--------20--------30--------40--------50---------
GYIPEAPRDGQAYVRKDGEWVLLSTFLGSSGNEQELLELDKWASLWNWFNITNWLWYIK
  | || ||||||||||||||||||||    ||||| ||| |||||| |||||||||||
..I.EA.RDGQAYVRKDGEWVLLSTFL....NEQEL.ELD.WASLWN.FNITNWLWYIK

Entity_assembly_ID: B, Chain length: 59, Sequence coverage: 81.4%

--------10--------20--------30--------40--------50---------
GYIPEAPRDGQAYVRKDGEWVLLSTFLGSSGNEQELLELDKWASLWNWFNITNWLWYIK
  | || ||||||||||||||||||||    ||||| ||| |||||| |||||||||||
..I.EA.RDGQAYVRKDGEWVLLSTFL....NEQEL.ELD.WASLWN.FNITNWLWYIK

Entity_assembly_ID: C, Chain length: 59, Sequence coverage: 81.4%

--------10--------20--------30--------40--------50---------
GYIPEAPRDGQAYVRKDGEWVLLSTFLGSSGNEQELLELDKWASLWNWFNITNWLWYIK
  | || ||||||||||||||||||||    ||||| ||| |||||| |||||||||||
..I.EA.RDGQAYVRKDGEWVLLSTFL....NEQEL.ELD.WASLWN.FNITNWLWYIK

Total number of restraints: 144
Potential type of restraints: undefined (144)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None
- Chain_ID: B
  None
- Chain_ID: C
  None

Keywords gp41, HIV-1, MPER

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Found 1 Document (0.799 seconds)

BMRB: 19215

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. gp41-M-MAT, : 1 : 1 : 3 entities Detail

Experiments performed 5 experiments Detail

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Instrument

Sample

Instrument

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NMR combined restraints 5 contents Detail