PDB-3bp9: Structure of B-tropic MLV capsid N-terminal domain

ID or keywords:

Entry

Database: PDB / ID: 3bp9

Title

Structure of B-tropic MLV capsid N-terminal domain

Components

Gag protein

Keywords

VIRAL PROTEIN / Capsid / Hexamer / MLV / Metal-binding / Zinc-finger

Function / homology

Function and homology information

virion assembly / viral budding via host ESCRT complex / host multivesicular body / viral nucleocapsid / structural constituent of virion / nucleic acid binding / host cell plasma membrane / RNA binding / zinc ion binding / membrane
Similarity search - Function

Biological species

Murine leukemia virus

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Gulnahar, M.B. / Dodding, M.P. / Goldstone, D.C. / Haire, L.F. / Stoye, J.P. / Taylor, I.A.

Citation

Journal: J.Mol.Biol. / Year: 2008
Title: Structure of B-MLV capsid amino-terminal domain reveals key features of viral tropism, gag assembly and core formation
Authors: Mortuza, G.B. / Dodding, M.P. / Goldstone, D.C. / Haire, L.F. / Stoye, J.P. / Taylor, I.A.

History

Deposition	Dec 18, 2007	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Feb 12, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Non-polymer description / Version format compliance
Revision 1.2	Nov 1, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3bp9.cif.gz	587.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3bp9.ent.gz	487.1 KB	Display	PDB format
PDBx/mmJSON format	3bp9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bp/3bp9 ftp://data.pdbj.org/pub/pdb/validation_reports/bp/3bp9	HTTPS FTP

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Related structure data

Related structure data	1u7kS S: Starting model for refinement
Similar structure data	1u7k-d 2gid-2 2gid-1 2gia-d 3fbn-3 5xty-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

1u7kS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: Gag protein

B: Gag protein

C: Gag protein

D: Gag protein

E: Gag protein

F: Gag protein

G: Gag protein

H: Gag protein

I: Gag protein

J: Gag protein

K: Gag protein

L: Gag protein

M: Gag protein

N: Gag protein

O: Gag protein

P: Gag protein

Q: Gag protein

R: Gag protein

S: Gag protein

T: Gag protein

U: Gag protein

V: Gag protein

X: Gag protein

Y: Gag protein

hetero molecules

384 kDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Gag protein

B: Gag protein

C: Gag protein

D: Gag protein

E: Gag protein

F: Gag protein

hetero molecules

defined by author
96.3 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

G: Gag protein

H: Gag protein

I: Gag protein

J: Gag protein

K: Gag protein

L: Gag protein

hetero molecules

defined by author
96.3 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

M: Gag protein

N: Gag protein

O: Gag protein

P: Gag protein

Q: Gag protein

R: Gag protein

defined by author
95.9 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

S: Gag protein

T: Gag protein

U: Gag protein

V: Gag protein

X: Gag protein

Y: Gag protein

defined by author
95.9 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	86.264, 86.832, 152.360
Angle α, β, γ (deg.)	89.120, 90.040, 60.260
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	PRO	PRO	LEU	LEU	A	A	1 - 4	1 - 4
2	1	PRO	PRO	LEU	LEU	B	B	1 - 4	1 - 4
3	1	PRO	PRO	LEU	LEU	C	C	1 - 4	1 - 4
4	1	PRO	PRO	LEU	LEU	D	D	1 - 4	1 - 4
5	1	PRO	PRO	LEU	LEU	E	E	1 - 4	1 - 4
6	1	PRO	PRO	LEU	LEU	F	F	1 - 4	1 - 4
7	1	PRO	PRO	LEU	LEU	G	G	1 - 4	1 - 4
8	1	PRO	PRO	LEU	LEU	H	H	1 - 4	1 - 4
9	1	PRO	PRO	LEU	LEU	I	I	1 - 4	1 - 4
10	1	PRO	PRO	LEU	LEU	J	J	1 - 4	1 - 4
11	1	PRO	PRO	LEU	LEU	K	K	1 - 4	1 - 4
12	1	PRO	PRO	LEU	LEU	L	L	1 - 4	1 - 4
13	1	PRO	PRO	LEU	LEU	M	M	1 - 4	1 - 4
14	1	PRO	PRO	LEU	LEU	N	N	1 - 4	1 - 4
15	1	PRO	PRO	LEU	LEU	O	O	1 - 4	1 - 4
16	1	PRO	PRO	LEU	LEU	P	P	1 - 4	1 - 4
17	1	PRO	PRO	LEU	LEU	Q	Q	1 - 4	1 - 4
18	1	PRO	PRO	LEU	LEU	R	R	1 - 4	1 - 4
19	1	PRO	PRO	LEU	LEU	S	S	1 - 4	1 - 4
20	1	PRO	PRO	LEU	LEU	T	T	1 - 4	1 - 4
21	1	PRO	PRO	LEU	LEU	U	U	1 - 4	1 - 4
22	1	PRO	PRO	LEU	LEU	V	V	1 - 4	1 - 4
23	1	PRO	PRO	LEU	LEU	X	W	1 - 4	1 - 4
24	1	PRO	PRO	LEU	LEU	Y	X	1 - 4	1 - 4
25	2	PHE	PHE	ARG	ARG	A	A	15 - 80	15 - 80
26	2	PHE	PHE	ARG	ARG	B	B	15 - 80	15 - 80
27	2	PHE	PHE	ARG	ARG	C	C	15 - 80	15 - 80
28	2	PHE	PHE	ARG	ARG	D	D	15 - 80	15 - 80
29	2	PHE	PHE	ARG	ARG	E	E	15 - 80	15 - 80
30	2	PHE	PHE	ARG	ARG	F	F	15 - 80	15 - 80
31	2	PHE	PHE	ARG	ARG	G	G	15 - 80	15 - 80
32	2	PHE	PHE	ARG	ARG	H	H	15 - 80	15 - 80
33	2	PHE	PHE	ARG	ARG	I	I	15 - 80	15 - 80
34	2	PHE	PHE	ARG	ARG	J	J	15 - 80	15 - 80
35	2	PHE	PHE	ARG	ARG	K	K	15 - 80	15 - 80
36	2	PHE	PHE	ARG	ARG	L	L	15 - 80	15 - 80
37	2	PHE	PHE	ARG	ARG	M	M	15 - 80	15 - 80
38	2	PHE	PHE	ARG	ARG	N	N	15 - 80	15 - 80
39	2	PHE	PHE	VAL	VAL	O	O	15 - 79	15 - 79
40	2	PHE	PHE	ARG	ARG	P	P	15 - 80	15 - 80
41	2	PHE	PHE	ARG	ARG	Q	Q	15 - 80	15 - 80
42	2	PHE	PHE	VAL	VAL	R	R	15 - 79	15 - 79
43	2	PHE	PHE	ARG	ARG	S	S	15 - 80	15 - 80
44	2	PHE	PHE	ARG	ARG	T	T	15 - 80	15 - 80
45	2	PHE	PHE	ARG	ARG	U	U	15 - 80	15 - 80
46	2	PHE	PHE	VAL	VAL	V	V	15 - 79	15 - 79
47	2	PHE	PHE	ARG	ARG	X	W	15 - 80	15 - 80
48	2	PHE	PHE	VAL	VAL	Y	X	15 - 79	15 - 79
49	3	PRO	PRO	ARG	ARG	A	A	90 - 131	90 - 131
50	3	PRO	PRO	ARG	ARG	B	B	90 - 131	90 - 131
51	3	PRO	PRO	ARG	ARG	C	C	90 - 131	90 - 131
52	3	PRO	PRO	ARG	ARG	D	D	90 - 131	90 - 131
53	3	PRO	PRO	ARG	ARG	E	E	90 - 131	90 - 131
54	3	PRO	PRO	ARG	ARG	F	F	90 - 131	90 - 131
55	3	PRO	PRO	ARG	ARG	G	G	90 - 131	90 - 131
56	3	PRO	PRO	ARG	ARG	H	H	90 - 131	90 - 131
57	3	PRO	PRO	ARG	ARG	I	I	90 - 131	90 - 131
58	3	PRO	PRO	ARG	ARG	J	J	90 - 131	90 - 131
59	3	PRO	PRO	ARG	ARG	K	K	90 - 131	90 - 131
60	3	PRO	PRO	ARG	ARG	L	L	90 - 131	90 - 131
61	3	PRO	PRO	ARG	ARG	M	M	90 - 131	90 - 131
62	3	PRO	PRO	ARG	ARG	N	N	90 - 131	90 - 131
63	3	PRO	PRO	ARG	ARG	O	O	90 - 131	90 - 131
64	3	PRO	PRO	ARG	ARG	P	P	90 - 131	90 - 131
65	3	PRO	PRO	ARG	ARG	Q	Q	90 - 131	90 - 131
66	3	PRO	PRO	ARG	ARG	R	R	90 - 131	90 - 131
67	3	PRO	PRO	ARG	ARG	S	S	90 - 131	90 - 131
68	3	PRO	PRO	ARG	ARG	T	T	90 - 131	90 - 131
69	3	GLU	GLU	ARG	ARG	U	U	92 - 131	92 - 131
70	3	GLU	GLU	ARG	ARG	V	V	92 - 131	92 - 131
71	3	PRO	PRO	ARG	ARG	X	W	90 - 131	90 - 131
72	3	PRO	PRO	ARG	ARG	Y	X	90 - 131	90 - 131

#1: Protein	... Gag protein Mass: 15977.679 Da / Num. of mol.: 24 / Fragment: UNP residues 215-346 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Murine leukemia virus / Genus: Gammaretrovirus / Gene: Gag / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9WHV6, UniProt: P03336*PLUS
#2: Chemical	ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL Mass: 60.095 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₃H₈O / Comment: alkaloid*YM
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.58 Å³/Da / Density % sol: 52.39 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 13-16% PEG 3350, 100mM sodium citrate pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 2.6→20 Å / Num. obs: 114996

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Processing

Software

Name	Version	Classification	NB
REFMAC	5.2.0019	refinement
PDB_EXTRACT	3.004	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U7K

1u7k

Resolution: 2.6→17.16 Å / Cor.coef. F_o:F_c: 0.934 / Cor.coef. F_o:F_c free: 0.885 / SU B: 13.26 / SU ML: 0.282 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.935 / ESU R Free: 0.373 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.292	5709	5 %	RANDOM
R_work	0.222	-	-	-
obs	0.226	113995	96.55 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 48.957 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.07 Å²	0.03 Å²	-0.03 Å²
2-	-	0.02 Å²	0.14 Å²
3-	-	-	0.02 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→17.16 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	24197	0	56	289	24542

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.021	24864
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	16720
X-RAY DIFFRACTION	r_angle_refined_deg	1.431	1.961	33901
X-RAY DIFFRACTION	r_angle_other_deg	0.96	3	40664
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.442	5	3034
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.699	24.749	1253
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.428	15	3915
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.475	15	173
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	3703
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	27850
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4859
X-RAY DIFFRACTION	r_nbd_refined	0.242	0.2	6684
X-RAY DIFFRACTION	r_nbd_other	0.192	0.2	16845
X-RAY DIFFRACTION	r_nbtor_refined	0.19	0.2	11908
X-RAY DIFFRACTION	r_nbtor_other	0.09	0.2	12893
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.164	0.2	821
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.038	0.2	9
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.201	0.2	28
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.317	0.2	85
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.136	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	0.691	1.5	15587
X-RAY DIFFRACTION	r_mcbond_other	0.125	1.5	6209
X-RAY DIFFRACTION	r_mcangle_it	1.225	2	24448
X-RAY DIFFRACTION	r_scbond_it	1.504	3	10665
X-RAY DIFFRACTION	r_scangle_it	2.371	4.5	9449

Refine LS restraints NCS

Ens-ID: 1 / Number: 1327 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	LOOSE POSITIONAL	0.48	5
2	B	LOOSE POSITIONAL	0.41	5
3	C	LOOSE POSITIONAL	0.65	5
4	D	LOOSE POSITIONAL	0.44	5
5	E	LOOSE POSITIONAL	0.5	5
6	F	LOOSE POSITIONAL	0.41	5
7	G	LOOSE POSITIONAL	0.56	5
8	H	LOOSE POSITIONAL	0.45	5
9	I	LOOSE POSITIONAL	0.46	5
10	J	LOOSE POSITIONAL	0.43	5
11	K	LOOSE POSITIONAL	0.53	5
12	L	LOOSE POSITIONAL	0.42	5
13	M	LOOSE POSITIONAL	0.51	5
14	N	LOOSE POSITIONAL	0.52	5
15	O	LOOSE POSITIONAL	0.58	5
16	P	LOOSE POSITIONAL	0.62	5
17	Q	LOOSE POSITIONAL	0.55	5
18	R	LOOSE POSITIONAL	0.68	5
19	S	LOOSE POSITIONAL	0.48	5
20	T	LOOSE POSITIONAL	0.54	5
21	U	LOOSE POSITIONAL	0.59	5
22	V	LOOSE POSITIONAL	0.61	5
23	X	LOOSE POSITIONAL	0.54	5
24	Y	LOOSE POSITIONAL	0.58	5
1	A	LOOSE THERMAL	3.37	10
2	B	LOOSE THERMAL	9.38	10
3	C	LOOSE THERMAL	9.48	10
4	D	LOOSE THERMAL	9.44	10
5	E	LOOSE THERMAL	7.29	10
6	F	LOOSE THERMAL	9.25	10
7	G	LOOSE THERMAL	3.12	10
8	H	LOOSE THERMAL	9.59	10
9	I	LOOSE THERMAL	10.08	10
10	J	LOOSE THERMAL	9.45	10
11	K	LOOSE THERMAL	7.2	10
12	L	LOOSE THERMAL	9.54	10
13	M	LOOSE THERMAL	4.6	10
14	N	LOOSE THERMAL	5.03	10
15	O	LOOSE THERMAL	9.92	10
16	P	LOOSE THERMAL	9.37	10
17	Q	LOOSE THERMAL	7.47	10
18	R	LOOSE THERMAL	9.51	10
19	S	LOOSE THERMAL	4.88	10
20	T	LOOSE THERMAL	5.35	10
21	U	LOOSE THERMAL	9.92	10
22	V	LOOSE THERMAL	9.49	10
23	X	LOOSE THERMAL	7.28	10
24	Y	LOOSE THERMAL	9.87	10

LS refinement shell

Resolution: 2.6→2.668 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.383	424	-
R_work	0.288	7877	-
all	-	8301	-
obs	-	-	95.52 %

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