PDB-4auv: Crystal Structure of the BRMS1 N-terminal region

ID or keywords:

Entry

Database: PDB / ID: 4auv

Title

Crystal Structure of the BRMS1 N-terminal region

Components

BREAST CANCER METASTASIS SUPPRESSOR 1

Keywords

APOPTOSIS / BRMS1 / METASTASIS SUPPRESSORS

Function / homology

Function and homology information

positive regulation of anoikis / positive regulation of protein deacetylation / negative regulation of stem cell population maintenance / Sin3-type complex / positive regulation of stem cell population maintenance / negative regulation of NF-kappaB transcription factor activity /

NF-kappaB binding / negative regulation of cell migration / HDACs deacetylate histones / negative regulation of transforming growth factor beta receptor signaling pathway ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIRAS / Resolution: 1.999 Å

Authors

Spinola-Amilibia, M. / Rivera, J. / Ortiz-Lombardia, M. / Romero, A. / Neira, J.L. / Bravo, J.

Citation

Journal: J.Mol.Biol. / Year: 2013
Title: Brms151-98 and Brms151-84 are Crystal Oligomeric Coiled Coils with Different Oligomerization States, which Behave as Disordered Protein Fragments in Solution.
Authors: Spinola-Amilibia, M. / Rivera, J. / Ortiz-Lombardia, M. / Romero, A. / Neira, J.L. / Bravo, J.

History

Deposition	May 22, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 20, 2013	Provider: repository / Type: Initial release
Revision 1.1	Apr 3, 2013	Group: Database references
Revision 1.2	Jun 12, 2013	Group: Database references
Revision 1.3	Nov 6, 2019	Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software Item: _pdbx_database_status.status_code_sf / _software.name / _software.version

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4auv.cif.gz	104.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4auv.ent.gz	89.4 KB	Display	PDB format
PDBx/mmJSON format	4auv.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/au/4auv ftp://data.pdbj.org/pub/pdb/validation_reports/au/4auv	HTTPS FTP

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Related structure data

Related structure data	2xus
Similar structure data	5e54-2 2mvg-d 3rkf-4 4fen-d 7crs-d 2or1-d 6jyd-d 6aba-d 5azd-2 4fej-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

2xus

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#4 - Apr 2000 Collagen similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

A: BREAST CANCER METASTASIS SUPPRESSOR 1

B: BREAST CANCER METASTASIS SUPPRESSOR 1

C: BREAST CANCER METASTASIS SUPPRESSOR 1

D: BREAST CANCER METASTASIS SUPPRESSOR 1

E: BREAST CANCER METASTASIS SUPPRESSOR 1

F: BREAST CANCER METASTASIS SUPPRESSOR 1

G: BREAST CANCER METASTASIS SUPPRESSOR 1

H: BREAST CANCER METASTASIS SUPPRESSOR 1

hetero molecules

35.2 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: BREAST CANCER METASTASIS SUPPRESSOR 1

B: BREAST CANCER METASTASIS SUPPRESSOR 1

D: BREAST CANCER METASTASIS SUPPRESSOR 1

E: BREAST CANCER METASTASIS SUPPRESSOR 1

hetero molecules

A: BREAST CANCER METASTASIS SUPPRESSOR 1

B: BREAST CANCER METASTASIS SUPPRESSOR 1

D: BREAST CANCER METASTASIS SUPPRESSOR 1

E: BREAST CANCER METASTASIS SUPPRESSOR 1

hetero molecules

defined by software
35.3 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: BREAST CANCER METASTASIS SUPPRESSOR 1

H: BREAST CANCER METASTASIS SUPPRESSOR 1

hetero molecules

C: BREAST CANCER METASTASIS SUPPRESSOR 1

H: BREAST CANCER METASTASIS SUPPRESSOR 1

hetero molecules

F: BREAST CANCER METASTASIS SUPPRESSOR 1

G: BREAST CANCER METASTASIS SUPPRESSOR 1

F: BREAST CANCER METASTASIS SUPPRESSOR 1

G: BREAST CANCER METASTASIS SUPPRESSOR 1

defined by software
35.1 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	3_655	-x+1,y,-z+1/2	1
crystal symmetry operation	6_554	-x+1/2,-y+1/2,z-1/2	1
crystal symmetry operation	8_556	x+1/2,-y+1/2,-z+1	1

3

C: BREAST CANCER METASTASIS SUPPRESSOR 1

H: BREAST CANCER METASTASIS SUPPRESSOR 1

hetero molecules

C: BREAST CANCER METASTASIS SUPPRESSOR 1

H: BREAST CANCER METASTASIS SUPPRESSOR 1

hetero molecules

defined by software
17.6 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

F: BREAST CANCER METASTASIS SUPPRESSOR 1

G: BREAST CANCER METASTASIS SUPPRESSOR 1

F: BREAST CANCER METASTASIS SUPPRESSOR 1

G: BREAST CANCER METASTASIS SUPPRESSOR 1

defined by software
17.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	42.636, 191.274, 71.940
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	C-2026- HOH
2	1	D-2004- HOH

Noncrystallographic symmetry (NCS)

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.996, -0.0407, 0.0799), (0.079, 0.0243, 0.9966), (-0.0425, 0.9989, -0.021)	18.2334, -37.0231, 37.0302
2	given	(-0.9603, -0.0799, -0.2673), (-0.1365, -0.7012, 0.6998), (-0.2434, 0.7085, 0.6625)	39.8143, 22.1001, -3.4031
3	given	(0.1054, 0.4145, 0.9039), (-0.1189, 0.9077, -0.4024), (-0.9873, -0.0651, 0.145)	-36.4774, 20.983, 50.2384
4	given	(-0.0978, 0.9409, 0.3243), (-0.0125, -0.327, 0.9449), (0.9951, 0.0883, 0.0438)	-13.6401, -30.3364, 32.7432
5	given	(-0.0567, 0.4284, -0.9018), (0.0431, -0.9014, -0.4309), (-0.9975, -0.0633, 0.0327)	24.5406, 72.059, 45.8896
6	given	(0.9761, -0.1007, -0.1927), (-0.2078, -0.6923, -0.691), (-0.0638, 0.7145, -0.6967)	26.5865, 71.7009, 37.5016
7	given	(-0.232, 0.3457, 0.9092), (0.051, -0.9291, 0.3663), (0.9714, 0.1314, 0.1979)	-29.6468, 40.1937, 15.7578

#1: Protein/peptide	BREAST CANCER METASTASIS SUPPRESSOR 1 Mass: 4374.907 Da / Num. of mol.: 8 / Fragment: RESIDUES 51-84 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28-6XHIS-SMT3/BRMS151-84 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: Q9HCU9
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-ACY / ACETIC ACID / Acetic acid Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₄O₂
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.33 Å³/Da / Density % sol: 47.2 % / Description: NONE
Crystal grow	pH: 4.3 Details: 0.1 M SODIUM ACETATE PH 4.3, 0.2 M AMMONIUM SULPHATE, 2 % PEG 4000

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source	Site	Beamline	ID	Wavelength
SYNCHROTRON	ESRF	ID14-1	1	0.934
SYNCHROTRON	ESRF	ID23-1	2	0.9729

Detector

Type	ID	Detector	Date	Details
ADSC QUANTUM 210	1	CCD	Aug 28, 2006	MIRRORS
ADSC QUANTUM 315r	2	CCD

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	ESRF MONOCHROMATOR AND TORODIAL FOCUSING MIRROR	SINGLE WAVELENGTH	M	x-ray	1
2		SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.934	1
2	0.9729	1

Reflection

Resolution: 2→95.56 Å / Num. obs: 20344 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 7.18 % / B_iso Wilson estimate: 38.1 Å² / R_merge(I) obs: 0.05 / Net I/σ(I): 6.66

Reflection shell

Resolution: 2→2.11 Å / Redundancy: 3.87 % / R_merge(I) obs: 0.2 / Mean I/σ(I) obs: 1.11 / % possible all: 94.7

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Processing

Software

Name	Version	Classification
REFMAC	5.6.0117	refinement
MOSFLM		data reduction
SCALA		data scaling
SHELXDE		phasing

Refinement

Method to determine structure:

SIRAS
Starting model: NONE

Resolution: 1.999→95.637 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.901 / SU B: 7.121 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2585	1031	5.13 %	RANDOM
R_work	0.1925	-	-	-
obs	0.196	20325	99.311 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK

Displacement parameters

B_iso mean: 24.926 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.417 Å²	0 Å²	0 Å²
2-	-	-0.932 Å²	0 Å²
3-	-	-	1.35 Å²

Refinement step

Cycle: LAST / Resolution: 1.999→95.637 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1763	0	10	153	1926

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.019	1867
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.061	2.026	2480
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.615	5	224
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.464	24.771	109
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.942	15	442
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.436	15	21
X-RAY DIFFRACTION	r_chiral_restr	0.14	0.2	262
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	1372
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.284	0.2	1047
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.308	0.2	1247
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.157	0.2	46
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	4.46	3.784	1866
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	5.766	5.756	2468
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	9.183	11.395	796
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	10.059	17.446	2185
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.999→2.051 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.243	65	-
R_work	0.217	1197	-
obs	-	-	92.117 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.5142	1.6552	0.5093	15.4203	0.4202	0.8968	0.1371	0.0217	-0.0796	-0.0325	-0.1067	-0.7344	0.1386	0.0926	-0.0303	0.1186	0.0019	0.0398	0.0393	0.0352	0.1317	16.1826	7.995	40.8261
2	2.1624	-0.0399	-3.0807	3.8682	5.596	13.9527	0.0801	-0.1527	0.0106	-0.1655	-0.258	0.4191	-0.0858	0.0014	0.1778	0.2712	0.0461	-0.0086	0.1594	-0.0072	0.325	5.7834	5.5015	38.3766
3	1.3406	1.1751	-1.8978	3.5387	-3.0369	6.0358	-0.0157	0.0156	-0.1084	-0.0239	-0.1092	-0.0587	-0.0772	-0.0956	0.1249	0.0199	0.0226	0.0246	0.0857	-0.003	0.056	14.0357	43.383	25.6449
4	5.0755	-3.7842	2.0767	18.2455	-10.182	10.2976	-0.2494	-0.5989	0.0396	0.947	0.2623	-0.2811	-0.7233	-0.2347	-0.0129	0.0754	-0.0024	-0.0065	0.1892	0.0421	0.034	15.1737	10.8466	51.5779
5	2.6492	1.5513	-4.7273	4.5925	-4.309	14.1461	-0.0052	-0.1077	-0.0798	0.1142	0.0888	0.7177	-0.0799	0.105	-0.0837	0.1315	0.0286	0.1436	0.0761	0.1035	0.312	5.7371	16.4888	46.531
6	3.4943	-2.1438	-0.8998	11.5411	4.5976	4.9019	-0.0249	0.4508	0.1795	-0.2018	-0.1708	-0.0211	-0.1727	0.031	0.1957	0.0091	-0.0075	-0.0062	0.1635	0.0601	0.0391	1.828	52.7168	33.9119
7	1.0856	0.8629	1.1173	5.76	6.5653	10.596	-0.2043	0.1334	0.0969	0.0072	-0.0194	-0.0269	-0.188	0.2135	0.2237	0.0652	-0.0145	-0.0507	0.14	0.0497	0.1112	3.217	52.6743	47.991
8	4.507	-1.9548	-0.4099	13.2888	-5.5004	5.8575	-0.0411	-0.0625	0.359	0.4006	-0.1402	-0.3889	-0.4185	0.157	0.1813	0.0855	-0.0098	-0.0073	0.1439	-0.0294	0.0455	13.2841	50.7499	34.2395

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	50 - 84
2	X-RAY DIFFRACTION	2	B	58 - 84
3	X-RAY DIFFRACTION	3	C	50 - 84
4	X-RAY DIFFRACTION	4	D	58 - 75
5	X-RAY DIFFRACTION	5	E	57 - 77
6	X-RAY DIFFRACTION	6	F	54 - 76
7	X-RAY DIFFRACTION	7	G	58 - 84
8	X-RAY DIFFRACTION	8	H	58 - 79

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