PDB-7zac: Sam68 - Yorodumi

ID or keywords:

Entry

Database: PDB / ID: 7zac

Title

Sam68

Components

KHDR1 protein

Keywords

RNA BINDING PROTEIN / Spinal Muscular Atrophy

Function / homology

Function and homology information

poly(A) binding / regulation of alternative mRNA splicing, via spliceosome / mRNA processing / mRNA binding / nucleus
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.08 Å

Authors

Nadal, M. / Fuentes-Prior, P.

Funding support

1items

Citation

Journal: Protein Sci. / Year: 2023
Title: Structure and function analysis of Sam68 and hnRNP A1 synergy in the exclusion of exon 7 from SMN2 transcripts.
Authors: Nadal, M. / Anton, R. / Dorca-Arevalo, J. / Estebanez-Perpina, E. / Tizzano, E.F. / Fuentes-Prior, P.

History

Deposition	Mar 22, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 1, 2023	Provider: repository / Type: Initial release
Revision 1.1	Feb 8, 2023	Group: Derived calculations Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 1.2	Apr 12, 2023	Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.3	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7zac.cif.gz	41.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7zac.ent.gz		Display	PDB format
PDBx/mmJSON format	7zac.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/za/7zac ftp://data.pdbj.org/pub/pdb/validation_reports/za/7zac	HTTPS FTP

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Related structure data

Related structure data	7z89C 7z8aC 7z9aC 7z9bC 7zabC 7zafC 7zamC 5emoS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#86 - Feb 2007 Exosomes similarity (2)

Deposited unit

AAA: KHDR1 protein

hetero molecules

13.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: KHDR1 protein

hetero molecules

AAA: KHDR1 protein

hetero molecules

defined by author&software
Evidence: gel filtration
27.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	69.567, 69.567, 81.740
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	91
Space group name H-M	P4₁22

Components on special symmetry positions

ID	Model	Components
1	1	AAA-1139- HOH

#1: Protein	KHDR1 protein Mass: 13141.489 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Khdrbs1, EURGUL_R11941 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7L4CZV7
#2: Chemical	ChemComp-NO3 / NITRATE ION Mass: 62.005 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: NO₃
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.76 Å³/Da / Density % sol: 67.31 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Ammonium sulfate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9787 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9787 Å / Relative weight: 1
Reflection	Resolution: 2.08→52.98 Å / Num. obs: 12375 / % possible obs: 97.4 % / Redundancy: 14.5 % / CC_1/2: 0.999 / Net I/σ(I): 24
Reflection shell	Resolution: 2.08→2.13 Å / Num. unique obs: 966 / CC_1/2: 0.765

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5EMO

5emo

Resolution: 2.08→52.98 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.948 / SU B: 5.076 / SU ML: 0.129 / Cross valid method: FREE R-VALUE / ESU R: 0.152 / ESU R Free: 0.158 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.2522	607	4.916 %
R_work	0.1948	11740	-
all	0.198	-	-
obs	-	12347	97.458 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 60.74 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.208 Å²	0 Å²	0 Å²
2-	-	-1.208 Å²	0 Å²
3-	-	-	2.416 Å²

Refinement step

Cycle: LAST / Resolution: 2.08→52.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	921	0	52	48	1021

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	980
X-RAY DIFFRACTION	r_angle_refined_deg	1.779	1.66	1291
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.372	5	114
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.43	23.182	44
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.588	15	187
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.323	15	4
X-RAY DIFFRACTION	r_chiral_restr	0.115	0.2	113
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	718
X-RAY DIFFRACTION	r_nbd_refined	0.223	0.2	393
X-RAY DIFFRACTION	r_nbtor_refined	0.319	0.2	637
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.125	0.2	42
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.203	0.2	50
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.297	0.2	7
X-RAY DIFFRACTION	r_mcbond_it	4.724	5.459	459
X-RAY DIFFRACTION	r_mcangle_it	5.816	8.162	572
X-RAY DIFFRACTION	r_scbond_it	7.883	6.371	520
X-RAY DIFFRACTION	r_scangle_it	10.683	9.098	719
X-RAY DIFFRACTION	r_lrange_it	11.396	105.367	3708

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.08-2.131	0.345	52	0.304	871	X-RAY DIFFRACTION	100
2.131-2.189	0.441	46	0.285	841	X-RAY DIFFRACTION	100
2.189-2.253	0.304	38	0.283	706	X-RAY DIFFRACTION	86.0116
2.253-2.322	0.28	32	0.234	673	X-RAY DIFFRACTION	83.1368
2.322-2.398	0.32	44	0.217	774	X-RAY DIFFRACTION	100
2.398-2.482	0.314	33	0.206	755	X-RAY DIFFRACTION	100
2.482-2.576	0.306	41	0.222	722	X-RAY DIFFRACTION	99.8691
2.576-2.681	0.338	35	0.247	707	X-RAY DIFFRACTION	100
2.681-2.8	0.386	27	0.248	678	X-RAY DIFFRACTION	100
2.8-2.936	0.355	31	0.236	659	X-RAY DIFFRACTION	100
2.936-3.095	0.281	37	0.24	607	X-RAY DIFFRACTION	100
3.095-3.282	0.261	30	0.213	600	X-RAY DIFFRACTION	100
3.282-3.508	0.204	33	0.195	548	X-RAY DIFFRACTION	100
3.508-3.788	0.2	22	0.171	527	X-RAY DIFFRACTION	100
3.788-4.149	0.195	26	0.168	430	X-RAY DIFFRACTION	89.2368
4.149-4.636	0.23	20	0.152	448	X-RAY DIFFRACTION	100
4.636-5.349	0.218	21	0.16	398	X-RAY DIFFRACTION	100
5.349-6.542	0.216	17	0.185	336	X-RAY DIFFRACTION	100
6.542-9.211	0.275	14	0.168	280	X-RAY DIFFRACTION	100
9.211-52.98	0.28	8	0.215	180	X-RAY DIFFRACTION	99.4709

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