PDB-7nyk: SH3 domain of JNK-interacting Protein 1 (JIP1)

ID or keywords:

Entry

Database: PDB / ID: 7nyk

Title

SH3 domain of JNK-interacting Protein 1 (JIP1)

Components

SH3 domain of JNK-interacting Protein 1 (JIP1)

Keywords

SIGNALING PROTEIN / SH3 domain of JNK-interacting protein 1 (JIP1)

Function / homology

Function and homology information

dentate gyrus mossy fiber / regulation of CD8-positive, alpha-beta T cell proliferation / negative regulation of JUN kinase activity / MAP-kinase scaffold activity / JUN kinase binding /

protein kinase inhibitor activity / regulation of JNK cascade /

kinesin binding / negative regulation of intrinsic apoptotic signaling pathway / JNK cascade ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.45 Å

Authors

Perez, L.M. / Ielasi, F.S. / Palencia, A. / Jensen, M.R.

Funding support

France, 2items

Citation

Journal: Nature / Year: 2022
Title: Visualizing protein breathing motions associated with aromatic ring flipping.
Authors: Marino Perez, L. / Ielasi, F.S. / Bessa, L.M. / Maurin, D. / Kragelj, J. / Blackledge, M. / Salvi, N. / Bouvignies, G. / Palencia, A. / Jensen, M.R.

History

Deposition	Mar 22, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 22, 2021	Provider: repository / Type: Initial release
Revision 1.1	Mar 2, 2022	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Mar 9, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3	Jan 31, 2024	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7nyk.cif.gz	127 KB	Display	PDBx/mmCIF format
PDB format	pdb7nyk.ent.gz		Display	PDB format
PDBx/mmJSON format	7nyk.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ny/7nyk ftp://data.pdbj.org/pub/pdb/validation_reports/ny/7nyk	HTTPS FTP

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Related structure data

Related structure data	7nylC 7nymC 7nynC 7nyoC 7nzbC 7nzcC 7nzdC 2fpeS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7nzb-3 7nyn-4 4db5-d 2ywy-1 2ywz-d 2dnc-d 7dda-d 6vsv-d 2avg-d 4rah-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) 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	#88 - Apr 2007 Clathrin similarity (4)

Deposited unit

AAA: SH3 domain of JNK-interacting Protein 1 (JIP1)

BBB: SH3 domain of JNK-interacting Protein 1 (JIP1)

CCC: SH3 domain of JNK-interacting Protein 1 (JIP1)

DDD: SH3 domain of JNK-interacting Protein 1 (JIP1)

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

1

AAA: SH3 domain of JNK-interacting Protein 1 (JIP1)

BBB: SH3 domain of JNK-interacting Protein 1 (JIP1)

defined by author&software
Evidence: gel filtration, chain A forms a dimer with chain B chain C forms a dimer with chain D
15.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

CCC: SH3 domain of JNK-interacting Protein 1 (JIP1)

DDD: SH3 domain of JNK-interacting Protein 1 (JIP1)

defined by author&software
15.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	71.399, 82.128, 46.849
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	AAA-636- HOH
2	1	CCC-605- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	AAA
2	1	BBB
3	2	AAA
4	2	CCC
5	3	AAA
6	3	DDD
7	4	BBB
8	4	CCC
9	5	BBB
10	5	DDD
11	6	CCC
12	6	DDD

NCS domain segments:

End auth comp-ID: VAL / End label comp-ID: VAL

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	HIS	HIS	AAA	A	488 - 547	2 - 61
2	2	1	HIS	HIS	BBB	B	488 - 547	2 - 61
3	3	2	HIS	HIS	AAA	A	488 - 547	2 - 61
4	4	2	HIS	HIS	CCC	C	488 - 547	2 - 61
5	5	3	MET	MET	AAA	A	489 - 547	3 - 61
6	6	3	MET	MET	DDD	D	489 - 547	3 - 61
7	7	4	HIS	HIS	BBB	B	488 - 547	2 - 61
8	8	4	HIS	HIS	CCC	C	488 - 547	2 - 61
9	9	5	MET	MET	BBB	B	489 - 547	3 - 61
10	10	5	MET	MET	DDD	D	489 - 547	3 - 61
11	11	6	MET	MET	CCC	C	489 - 547	3 - 61
12	12	6	MET	MET	DDD	D	489 - 547	3 - 61

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein	SH3 domain of JNK-interacting Protein 1 (JIP1) / JIP-1 / JNK-interacting protein 1 / Islet-brain 1 / IB-1 / JNK MAP kinase scaffold protein 1 / ...JIP-1 / JNK-interacting protein 1 / Islet-brain 1 / IB-1 / JNK MAP kinase scaffold protein 1 / Mitogen-activated protein kinase 8-interacting protein 1 / C-Jun-amino-terminal kinase-interacting protein 1 Mass: 7526.367 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: GHM belong to expression vector pET28a / Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK8IP1, IB1, JIP1, PRKM8IP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UQF2, phosphoinositide 5-phosphatase
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

SH3 domain of JNK-interacting Protein 1 (JIP1) / JIP-1 / JNK-interacting protein 1 / Islet-brain 1 / IB-1 / JNK MAP kinase scaffold protein 1 / ...

Mass: 7526.367 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: GHM belong to expression vector pET28a / Source: (gene. exp.)

Homo sapiens (human) / Gene: MAPK8IP1, IB1, JIP1, PRKM8IP / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UQF2,

phosphoinositide 5-phosphatase

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.3 Å³/Da / Density % sol: 47 % / Description: 3D needless
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion / pH: 7.5 Details: 0.1 M HEPES pH 7.5; 1-5 PEG 400; 2-2.5 M Ammonium sulphate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.96546 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2020
Radiation	Monochromator: Silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.96546 Å / Relative weight: 1
Reflection	Resolution: 1.35→53.883 Å / Num. obs: 41308 / % possible obs: 91.8 % / Observed criterion σ(I): 1.5 / Redundancy: 4.6 % / CC_1/2: 0.993 / Net I/σ(I): 9.5
Reflection shell	Resolution: 1.356→1.48 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2066 / CC_1/2: 0.61

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Processing

Software

Name	Version	Classification
REFMAC	7.1.007	refinement
autoPROC		data reduction
autoPROC		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2FPE

2fpe

Resolution: 1.45→53.883 Å / Cor.coef. F_o:F_c: 0.973 / Cor.coef. F_o:F_c free: 0.955 / SU B: 4.52 / SU ML: 0.072 / Cross valid method: FREE R-VALUE / ESU R: 0.097 / ESU R Free: 0.086
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.215	2066	5.131 %
R_work	0.1565	38196	-
all	0.16	-	-
obs	-	40262	81.147 %

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: 25.32 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.969 Å²	-0 Å²	0 Å²
2-	-	1.907 Å²	0 Å²
3-	-	-	-0.939 Å²

Refinement step

Cycle: LAST / Resolution: 1.45→53.883 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2069	0	0	363	2432

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.013	2157
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	1901
X-RAY DIFFRACTION	r_angle_refined_deg	1.689	1.658	2942
X-RAY DIFFRACTION	r_angle_other_deg	1.418	1.573	4362
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.553	5	249
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	24.681	21.699	153
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.704	15	332
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.746	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	262
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	2480
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	544
X-RAY DIFFRACTION	r_nbd_refined	0.232	0.2	395
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.203	0.2	2001
X-RAY DIFFRACTION	r_nbtor_refined	0.179	0.2	1001
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	1134
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.199	0.2	245
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.079	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.252	0.2	23
X-RAY DIFFRACTION	r_nbd_other	0.235	0.2	60
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.288	0.2	32
X-RAY DIFFRACTION	r_mcbond_it	4.372	2.258	987
X-RAY DIFFRACTION	r_mcbond_other	4.337	2.251	986
X-RAY DIFFRACTION	r_mcangle_it	4.988	3.35	1230
X-RAY DIFFRACTION	r_mcangle_other	5.044	3.357	1231
X-RAY DIFFRACTION	r_scbond_it	5.808	2.762	1170
X-RAY DIFFRACTION	r_scbond_other	5.807	2.766	1171
X-RAY DIFFRACTION	r_scangle_it	6.844	3.991	1709
X-RAY DIFFRACTION	r_scangle_other	6.842	3.996	1710
X-RAY DIFFRACTION	r_lrange_it	6.956	27.982	2512
X-RAY DIFFRACTION	r_lrange_other	6.828	27.167	2425
X-RAY DIFFRACTION	r_rigid_bond_restr	3.393	3	4057
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.116	0.05	1930
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.083	0.05	1986
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.088	0.05	1909
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.126	0.05	1889
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.094	0.05	1929
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.11	0.05	1878

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	AAA	X-RAY DIFFRACTION	Local ncs	0.11581	0.05008
1	2	BBB	X-RAY DIFFRACTION	Local ncs	0.11581	0.05008
2	3	AAA	X-RAY DIFFRACTION	Local ncs	0.08276	0.05009
2	4	CCC	X-RAY DIFFRACTION	Local ncs	0.08276	0.05009
3	5	AAA	X-RAY DIFFRACTION	Local ncs	0.08816	0.05009
3	6	DDD	X-RAY DIFFRACTION	Local ncs	0.08816	0.05009
4	7	BBB	X-RAY DIFFRACTION	Local ncs	0.12626	0.05008
4	8	CCC	X-RAY DIFFRACTION	Local ncs	0.12626	0.05008
5	9	BBB	X-RAY DIFFRACTION	Local ncs	0.09352	0.05009
5	10	DDD	X-RAY DIFFRACTION	Local ncs	0.09352	0.05009
6	11	CCC	X-RAY DIFFRACTION	Local ncs	0.11011	0.05008
6	12	DDD	X-RAY DIFFRACTION	Local ncs	0.11011	0.05008

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.45-1.488	0.376	79	0.315	1294	0.319	3602	0.781	0.782	38.1177	0.304
1.488-1.528	0.321	98	0.263	1933	0.266	3537	0.848	0.88	57.4215	0.253
1.528-1.573	0.292	114	0.238	2098	0.24	3416	0.897	0.897	64.7541	0.225
1.573-1.621	0.279	114	0.199	2192	0.203	3340	0.895	0.921	69.0419	0.183
1.621-1.674	0.282	106	0.176	2240	0.181	3261	0.917	0.936	71.9411	0.158
1.674-1.733	0.268	126	0.16	2181	0.165	3114	0.909	0.944	74.0848	0.137
1.733-1.798	0.25	110	0.144	2229	0.148	3015	0.923	0.952	77.5788	0.122
1.798-1.871	0.258	132	0.158	2267	0.164	2936	0.918	0.938	81.7098	0.136
1.871-1.955	0.217	126	0.153	2399	0.156	2779	0.928	0.946	90.86	0.133
1.955-2.05	0.226	153	0.16	2523	0.164	2694	0.939	0.947	99.3318	0.141
2.05-2.161	0.286	123	0.161	2428	0.166	2556	0.911	0.944	99.8044	0.15
2.161-2.291	0.216	127	0.143	2286	0.147	2424	0.935	0.956	99.5462	0.142
2.291-2.449	0.216	132	0.136	2112	0.141	2289	0.938	0.959	98.0341	0.141
2.449-2.645	0.244	101	0.139	2038	0.144	2147	0.928	0.959	99.6274	0.149
2.645-2.897	0.19	106	0.134	1855	0.137	1965	0.954	0.967	99.7964	0.151
2.897-3.238	0.214	97	0.148	1684	0.151	1800	0.944	0.964	98.9444	0.172
3.238-3.736	0.183	79	0.149	1520	0.151	1608	0.965	0.97	99.4403	0.178
3.736-4.57	0.163	56	0.134	1292	0.135	1374	0.965	0.973	98.1077	0.187
4.57-6.44	0.187	47	0.175	1013	0.176	1082	0.967	0.97	97.9667	0.242
6.44-53.883	0.174	39	0.236	610	0.232	663	0.966	0.947	97.8884	0.336

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