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BMRB: 19458

2MCY

CR1-2-3

Authors

Park, H.J., Guariento, M.J., Maciejewski, M., Hauart, R., Tham, W., Cowman, A.F., Schmidt, C.Q., Martens, H., Liszewski, K.M., Hourcade, D., Barlow, P.N., Atkinson, J.P.

Assembly

Recombinant CR1 fragment, domains 2-3

Entity

1. Recombinant CR1 fragment, domains 2-3 (polymer), 136 monomers, 14662.37 Da Detail

EAEAKSCRNP PDPVNGMVHV IKGIQFGSQI KYSCTKGYRL IGSSSATCII SGDTVIWDTE TPICDRIPCG LPPTITNGDF ISTNRENFHY GSVVTYRCNP GSGGRKVFEL VGEPSIYCTS NDDQVGIWSG PAPQCI

Formula weight

14662.37 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 63.2 %, Completeness: 34.5 %, Completeness (bb): 45.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	34.5 % (519 of 1504)	34.5 % (269 of 779)	31.2 % (183 of 587)	48.6 % (67 of 138)
Backbone	45.7 % (363 of 794)	48.6 % (134 of 276)	41.5 % (163 of 393)	52.8 % (66 of 125)
Sidechain	26.6 % (221 of 831)	26.8 % (135 of 503)	27.0 % (85 of 315)	7.7 % (1 of 13)
Aromatic	11.6 % (13 of 112)	16.1 % (9 of 56)	7.4 % (4 of 54)	0.0 % (0 of 2)
Methyl	12.1 % (16 of 132)	13.6 % (9 of 66)	10.6 % (7 of 66)

1. CR1 2-3

EAEAKSCRNP PDPVNGMVHV IKGIQFGSQI KYSCTKGYRL IGSSSATCII SGDTVIWDTE TPICDRIPCG LPPTITNGDF ISTNRENFHY GSVVTYRCNP GSGGRKVFEL VGEPSIYCTS NDDQVGIWSG PAPQCI

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	CR1 2-3	[U-99% 13C; U-99% 15N]		0.8 mM
2	sodium phosphate	natural abundance		10 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 310 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
5	CR1 2-3	[U-99% 13C; U-99% 15N]		0.8 mM
6	sodium phosphate	natural abundance		10 mM
7	D2O	natural abundance		100 %

Protein Blocks Logo

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

Release date

2013-11-10

Citation

Using mutagenesis and structural biology to map the binding site for the Plasmodium falciparum merozoite protein PfRh4 on the human immune adherence receptor
Park, H., Guariento, M., Maciejewski, M., Hauhart, R., Tham, W., Cowman, A.F., Schmidt, C.Q., Mertens, H.D.T., Liszewski, M., Hourcade, D.E., Barlow, P.N., Atkinson, J.P.
J. Biol. Chem. (2014), 289, 450-463, PubMed 24214979 , DOI 10.1074/jbc.M113.520346 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 19459 released on 2013-11-10
Title CR1~1-2

Related entities 1. Recombinant CR1 fragment, domains 2-3, : 1 : 3 : 782 entities Detail

Interaction partners 1. Recombinant CR1 fragment, domains 2-3, : 7 interactors Detail

More details for 7 interactors identified by 1 citations

Experiments performed 9 experiments Detail

1 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	CR1 2-3	[U-99% 13C; U-99% 15N]		0.8 mM
2	sodium phosphate	natural abundance		10 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

2 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	CR1 2-3	[U-99% 13C; U-99% 15N]		0.8 mM
2	sodium phosphate	natural abundance		10 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

3 3D HBHA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	CR1 2-3	[U-99% 13C; U-99% 15N]		0.8 mM
2	sodium phosphate	natural abundance		10 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

4 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	CR1 2-3	[U-99% 13C; U-99% 15N]		0.8 mM
2	sodium phosphate	natural abundance		10 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

5 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	CR1 2-3	[U-99% 13C; U-99% 15N]		0.8 mM
2	sodium phosphate	natural abundance		10 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

6 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	CR1 2-3	[U-99% 13C; U-99% 15N]		0.8 mM
2	sodium phosphate	natural abundance		10 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

7 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	CR1 2-3	[U-99% 13C; U-99% 15N]		0.8 mM
2	sodium phosphate	natural abundance		10 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

8 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	CR1 2-3	[U-99% 13C; U-99% 15N]		0.8 mM
2	sodium phosphate	natural abundance		10 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

9 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 310 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
5	CR1 2-3	[U-99% 13C; U-99% 15N]		0.8 mM
6	sodium phosphate	natural abundance		10 mM
7	D2O	natural abundance		100 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19458_2mcy.nef
Input source #2: Coordindates	2mcy.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:63:CYS:SG	A:104:CYS:SG	unknown	unknown	2.002
A:90:CYS:SG	A:120:CYS:SG	unknown	reduced, CA 55.794, CB 30.6736 ppm	2.002
A:125:CYS:SG	A:174:CYS:SG	reduced, CA 61.9342, CB 31.233 ppm	reduced, CA 62.5483, CB 32.752 ppm	2.05
A:154:CYS:SG	A:191:CYS:SG	unknown, CA 42.9324 ppm	oxidized, CA 52.399, CB 43.6127 ppm	2.037

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

--60--------70--------80--------90-------100-------110-------120-------130-------140-------150------
EAEAKSCRNPPDPVNGMVHVIKGIQFGSQIKYSCTKGYRLIGSSSATCIISGDTVIWDTETPICDRIPCGLPPTITNGDFISTNRENFHYGSVVTYRCNP
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
EAEAKSCRNPPDPVNGMVHVIKGIQFGSQIKYSCTKGYRLIGSSSATCIISGDTVIWDTETPICDRIPCGLPPTITNGDFISTNRENFHYGSVVTYRCNP
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-160-------170-------180-------190--
GSGGRKVFELVGEPSIYCTSNDDQVGIWSGPAPQCI
||||||||||||||||||||||||||||||||||||
GSGGRKVFELVGEPSIYCTSNDDQVGIWSGPAPQCI
-------110-------120-------130------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	136	0	0	100.0

Content subtype: combined_19458_2mcy.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	468		58.1 (chain: A, length: 136)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	3167 (1)	noe	92.6 (chain: A, length: 136)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 136, Sequence coverage: 58.1%

--60--------70--------80--------90-------100-------110-------120-------130-------140-------150------
EAEAKSCRNPPDPVNGMVHVIKGIQFGSQIKYSCTKGYRLIGSSSATCIISGDTVIWDTETPICDRIPCGLPPTITNGDFISTNRENFHYGSVVTYRCNP
                                                         |||||||||||||||||||||||||||||||||||||||||||
.........................................................DTETPICDRIPCGLPPTITNGDFISTNRENFHYGSVVTYRCNP

-160-------170-------180-------190--
GSGGRKVFELVGEPSIYCTSNDDQVGIWSGPAPQCI
||||||||||||||||||||||||||||||||||||
GSGGRKVFELVGEPSIYCTSNDDQVGIWSGPAPQCI

Total number of assignments
- ¹H chemical shifts: 249
- ¹³C chemical shifts: 152
- ¹⁵N chemical shifts: 67

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
117	THR	HG1	1.3543
118	PRO	N	115.062
120	CYS	HG	1.7
124	PRO	N	118.433
128	PRO	N	104.6408
129	PRO	N	116.2587
130	THR	HG1	0.265
132	THR	HG1	0.7701
143	ASN	CG	25.139
148	SER	HG	1.3825
152	TYR	CG	27.972
156	PRO	N	116.6697
170	PRO	N	123.2787
178	ASP	CG	27.503
180	GLN	CD	50.8875
184	TRP	CG	25.208
185	SER	HG	1.7915
187	PRO	N	119.889
189	PRO	N	117.96

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	779	243	31.2
¹³C chemical shifts	587	147	25.0
¹⁵N chemical shifts	144	59	41.0

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	276	122	44.2
¹³C chemical shifts	272	75	27.6
¹⁵N chemical shifts	125	59	47.2

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	503	121	24.1
¹³C chemical shifts	315	72	22.9
¹⁵N chemical shifts	19	0	0.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	67	9	13.4
¹³C chemical shifts	67	7	10.4

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	56	9	16.1
¹³C chemical shifts	54	4	7.4
¹⁵N chemical shifts	2	0	0.0

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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 136, Sequence coverage: 92.6%
- Total number of restraints: 3160
- Weight of restraints: 1.0 (3160)
- Potential type of restraints: square-well-parabolic (3160)
- Range of distance target values: 2.08, 4.12 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords CCP, CR1, malaria, PfRh4, Plasmodium falciparum