PDB-2j6k: N-TERMINAL SH3 DOMAIN OF CMS (CD2AP HUMAN HOMOLOG)

ID or keywords:

Entry

Database: PDB / ID: 2j6k

Title

N-TERMINAL SH3 DOMAIN OF CMS (CD2AP HUMAN HOMOLOG)

Components

CD2-ASSOCIATED PROTEIN

Keywords

PROTEIN BINDING /

PHOSPHORYLATION / ADAPTOR PROTEIN / EGFR DOWNREGULATION / SH3 /

SH3 DOMAIN / SH3-BINDING / CD2 ASSOCIATED PROTEIN / CYTOSKELETAL REARRANGEMENTS / SURFACE ACTIVE PROTEIN /

SIGNALING PROTEIN

Function / homology

Function and homology information

negative regulation of small GTPase mediated signal transduction / transforming growth factor beta1 production / negative regulation of transforming growth factor beta1 production / response to transforming growth factor beta / immunological synapse formation / protein heterooligomerization / substrate-dependent cell migration, cell extension /

podosome / Nephrin family interactions / cell leading edge ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION / OTHER / Resolution: 2.77 Å

Authors

Moncalian, G. / Cardenes, N. / Deribe, Y.L. / Spinola-Amilibia, M. / Dikic, I. / Bravo, J.

Citation

Journal: J.Biol.Chem. / Year: 2006
Title: Atypical Polyproline Recognition by the Cms N- Terminal SH3 Domain.
Authors: Moncalian, G. / Cardenes, N. / Deribe, Y.L. / Spinola-Amilibia, M. / Dikic, I. / Bravo, J.

History

Deposition	Sep 29, 2006	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 11, 2006	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Jul 5, 2017	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2j6k.cif.gz	145.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2j6k.ent.gz	124.9 KB	Display	PDB format
PDBx/mmJSON format	2j6k.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/j6/2j6k ftp://data.pdbj.org/pub/pdb/validation_reports/j6/2j6k	HTTPS FTP

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Related structure data

Related structure data	2j6fC 2j6oC 2j7iC C: citing same article (ref.)
Similar structure data	2jm9-d 4rqm-2 6kg9-d 4ull-d 6s9y-3 6b29-3 1qkw-d 2ll4-d 2hy9-d 3m0q-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) 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) 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

2j6fC

2j6oC

2j7iC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#88 - Apr 2007 Clathrin similarity (1)

Deposited unit

A: CD2-ASSOCIATED PROTEIN

B: CD2-ASSOCIATED PROTEIN

C: CD2-ASSOCIATED PROTEIN

D: CD2-ASSOCIATED PROTEIN

E: CD2-ASSOCIATED PROTEIN

F: CD2-ASSOCIATED PROTEIN

G: CD2-ASSOCIATED PROTEIN

H: CD2-ASSOCIATED PROTEIN

I: CD2-ASSOCIATED PROTEIN

J: CD2-ASSOCIATED PROTEIN

K: CD2-ASSOCIATED PROTEIN

L: CD2-ASSOCIATED PROTEIN

hetero molecules

89 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: CD2-ASSOCIATED PROTEIN

hetero molecules

defined by author&software
7.44 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: CD2-ASSOCIATED PROTEIN

defined by author&software
7.41 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: CD2-ASSOCIATED PROTEIN

defined by author&software
7.41 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: CD2-ASSOCIATED PROTEIN

defined by author&software
7.41 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: CD2-ASSOCIATED PROTEIN

defined by author&software
7.41 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

F: CD2-ASSOCIATED PROTEIN

defined by author&software
7.41 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

7

G: CD2-ASSOCIATED PROTEIN

defined by author&software
7.41 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

8

H: CD2-ASSOCIATED PROTEIN

defined by author&software
7.41 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

9

I: CD2-ASSOCIATED PROTEIN

hetero molecules

defined by author&software
7.44 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

10

J: CD2-ASSOCIATED PROTEIN

defined by author&software
7.41 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

11

K: CD2-ASSOCIATED PROTEIN

defined by author&software
7.41 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

12

L: CD2-ASSOCIATED PROTEIN

defined by author&software
7.41 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	120.018, 120.018, 153.930
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	79
Space group name H-M	I4

Components on special symmetry positions

ID	Model	Components
1	1	A-1059- NA
2	1	I-1059- NA
3	1	I-2004- HOH
4	1	J-2011- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	E
4	1	F
5	1	K
6	1	L
1	2	C
2	2	D
3	2	G
4	2	H
5	2	I
6	2	J

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	3	A	1 - 60
2	1	1	3	B	1 - 60
3	1	1	3	E	1 - 60
4	1	1	3	F	1 - 60
5	1	1	3	K	1 - 60
6	1	1	3	L	1 - 60
1	1	2	3	C	1 - 60
2	1	2	3	D	1 - 60
3	1	2	3	G	1 - 60
4	1	2	3	H	1 - 60
5	1	2	3	I	1 - 60
6	1	2	3	J	1 - 60

NCS ensembles :

ID
1
2

#1: Protein	CD2-ASSOCIATED PROTEIN / CAS LIGAND WITH MULTIPLE SH3 DOMAINS / ADAPTER PROTEIN CMS Mass: 7412.285 Da / Num. of mol.: 12 / Fragment: SH3, RESIDUES 1-62 Source method: isolated from a genetically manipulated source Details: N-TERMINAL SH3 DOMAIN (SH3A) OF CD2- ASSOCIATED PROTEIN (CD2AP) OR CAS LIGAND WITH MULTIPLE SRC HOMOLOGY 3 DOMAINS (CMS) Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA (DE3) PLYS / References: UniProt: Q9Y5K6
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 95 / 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: 3.3 Å³/Da / Density % sol: 63 %
Crystal grow	pH: 6.1 Details: 0.1 M SODIUM CITRATE PH 6.1, 25% PEG 4000, 20% ISOPROPANOL

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Data collection

Diffraction	Mean temperature: 130 K
Diffraction source	Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
Detector	Type: MARRESEARCH / Detector: CCD / Date: May 30, 2006 / Details: MIRRORS
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.76→47.3 Å / Num. obs: 27491 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 3.47 % / B_iso Wilson estimate: 62.58 Å² / R_merge(I) obs: 0.1 / Net I/σ(I): 10.98
Reflection shell	Resolution: 2.76→2.79 Å / Redundancy: 3.26 % / R_merge(I) obs: 0.33 / Mean I/σ(I) obs: 0.95 / % possible all: 81

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MOSFLM		data reduction
TRUNCATE		data scaling

Refinement

Method to determine structure: OTHER / Resolution: 2.77→94.49 Å / Cor.coef. F_o:F_c: 0.91 / Cor.coef. F_o:F_c free: 0.853 / SU B: 28.857 / SU ML: 0.277 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.887 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.274	1385	5.08 %	RANDOM
R_work	0.208	-	-	-
obs	0.211	27491	99.8 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 30.32 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.468 Å²	0 Å²	0 Å²
2-	-	-0.468 Å²	0 Å²
3-	-	-	0.935 Å²

Refinement step

Cycle: LAST / Resolution: 2.77→94.49 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5712	0	2	95	5809

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	5894
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.465	1.955	7948
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.473	5	695
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.808	24.889	360
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.522	15	1099
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.133	15	49
X-RAY DIFFRACTION	r_chiral_restr	0.109	0.2	828
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	4589
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.216	0.2	2382
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.324	0.2	3900
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.143	0.2	205
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	0.223	0.2	167
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.205	0.2	40
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	0.312	1.5	3396
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.733	2	5496
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.629	3	2592
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.719	4.5	2440
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

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	223	tight positional	0.08	0.05
1	2	B	223	tight positional	0.07	0.05
1	3	E	223	tight positional	0.06	0.05
1	4	F	223	tight positional	0.05	0.05
1	5	K	223	tight positional	0.05	0.05
1	6	L	223	tight positional	0.05	0.05
2	1	C	221	tight positional	0.06	0.05
2	2	D	221	tight positional	0.07	0.05
2	3	G	221	tight positional	0.06	0.05
2	4	H	221	tight positional	0.06	0.05
2	5	I	221	tight positional	0.06	0.05
2	6	J	221	tight positional	0.06	0.05
1	1	A	223	loose positional	0.63	5
1	2	B	223	loose positional	0.43	5
1	3	E	223	loose positional	0.41	5
1	4	F	223	loose positional	0.42	5
1	5	K	223	loose positional	0.38	5
1	6	L	223	loose positional	0.46	5
2	1	C	213	loose positional	0.6	5
2	2	D	213	loose positional	0.5	5
2	3	G	213	loose positional	0.81	5
2	4	H	213	loose positional	0.37	5
2	5	I	213	loose positional	0.47	5
2	6	J	213	loose positional	0.49	5
1	1	A	223	tight thermal	0.12	0.5
1	2	B	223	tight thermal	0.09	0.5
1	3	E	223	tight thermal	0.1	0.5
1	4	F	223	tight thermal	0.09	0.5
1	5	K	223	tight thermal	0.09	0.5
1	6	L	223	tight thermal	0.08	0.5
2	1	C	221	tight thermal	0.11	0.5
2	2	D	221	tight thermal	0.1	0.5
2	3	G	221	tight thermal	0.08	0.5
2	4	H	221	tight thermal	0.09	0.5
2	5	I	221	tight thermal	0.08	0.5
2	6	J	221	tight thermal	0.09	0.5
1	1	A	223	loose thermal	2.1	10
1	2	B	223	loose thermal	2.16	10
1	3	E	223	loose thermal	1.6	10
1	4	F	223	loose thermal	2.01	10
1	5	K	223	loose thermal	2.27	10
1	6	L	223	loose thermal	1.61	10
2	1	C	213	loose thermal	2.09	10
2	2	D	213	loose thermal	1.86	10
2	3	G	213	loose thermal	1.74	10
2	4	H	213	loose thermal	1.93	10
2	5	I	213	loose thermal	1.64	10
2	6	J	213	loose thermal	1.89	10

LS refinement shell

Resolution: 12.31→94.49 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.465	17
R_work	0.402	308

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	4.2103	-0.37	-2.4187	2.6966	-0.4828	4.8675	-0.143	-0.3273	-0.1286	0.2082	0.1006	-0.0957	0.2231	0.0257	0.0424	-0.1621	0.0072	-0.0188	-0.1949	0.0088	-0.1651	48.5971	48.3474	1.1372
2	4.3326	-0.4857	0.094	5.5161	1.3375	6.9256	-0.1197	0.3366	-0.0573	-0.3584	0.0734	0.0269	0.0711	-0.4821	0.0462	-0.1673	-0.0262	-0.0156	-0.1031	-0.0377	-0.179	48.0745	48.4468	-23.4999
3	4.2715	0.2461	0.2389	9.0289	1.3874	6.7386	-0.1843	0.3572	-0.0097	0.0268	0.0437	-0.4319	0.2403	0.3852	0.1406	-0.1603	0.0404	0.0225	-0.1049	-0.0105	-0.1422	-23.9334	18.9935	9.0316
4	2.2137	-0.1372	0.3375	7.074	-0.4844	4.1734	-0.0084	0.1711	-0.2286	-0.2639	-0.0938	0.3349	0.2671	-0.4783	0.1022	-0.1586	-0.0273	-0.0113	-0.1264	0.0115	-0.1354	-45.8755	29.8072	8.0248
5	7.1933	0.1181	1.7167	7.0892	-5.131	8.7844	0.0771	-0.1584	-0.0277	0.1553	0.0565	0.4973	0.0858	-0.6952	-0.1335	-0.0935	-0.0331	0.0315	-0.1085	-0.0312	-0.1882	22.3238	17.2553	-47.3331
6	3.5305	-1.0064	0.5348	6.3547	-0.7566	6.2017	0.0849	-0.0709	0.024	0.2423	-0.1529	0.0596	-0.4015	0.2552	0.0679	-0.1038	-0.0489	0.0034	-0.132	-0.0447	-0.172	33.1061	39.308	-46.3563
7	8.6881	0.7415	-3.1904	7.7932	0.6001	8.6217	0.417	0.0436	0.8881	-0.1668	-0.0139	0.2966	-0.6049	-0.0592	-0.4032	-0.1706	0.0589	0.0718	-0.1385	0.0898	0.1901	10.772	56.0852	16.7467
8	7.607	1.0317	-0.7544	4.8324	0.6285	7.5681	-0.1744	0.2907	-0.1423	-0.3849	0.2411	0.3779	0.3236	-0.109	-0.0667	-0.1338	-0.0388	-0.0439	-0.0918	0.0456	-0.1092	-0.3896	34.0708	17.4207
9	7.1697	0.7622	-0.2422	6.4623	0.4609	5.7176	0.2471	-0.3908	0.1096	0.3812	-0.1459	0.2715	-0.2583	-0.1234	-0.1012	-0.0635	-0.0092	-0.0037	-0.1397	-0.0502	-0.147	0.9562	16.2892	-5.2966
10	10.0258	-0.518	0.9257	4.0359	0.5151	5.7009	0.062	0.0171	0.2123	-0.0953	-0.1324	-0.1446	-0.3601	-0.0296	0.0705	-0.0786	0.0188	-0.052	-0.2156	-0.0161	-0.1729	0.9354	16.2242	-29.6519
11	7.4384	0.9199	2.1644	7.9443	0.3552	2.9672	-0.071	-0.4332	-0.4669	0.4874	0.1492	-0.0251	0.2596	0.0313	-0.0783	-0.0861	0.0642	0.0478	-0.1002	0.0396	-0.1263	29.4834	67.1593	-38.012
12	6.0553	1.0921	1.759	12.1591	2.9317	5.0656	-0.1942	-0.7355	0.3145	0.6882	-0.1608	1.4356	-0.2129	-0.5423	0.3549	0.0281	0.0665	0.1911	0.0972	0.042	0.1521	7.5225	78.2947	-38.5514

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 58
2	X-RAY DIFFRACTION	2	B	2 - 58
3	X-RAY DIFFRACTION	3	C	2 - 58
4	X-RAY DIFFRACTION	4	D	2 - 58
5	X-RAY DIFFRACTION	5	E	2 - 58
6	X-RAY DIFFRACTION	6	F	2 - 58
7	X-RAY DIFFRACTION	7	G	2 - 58
8	X-RAY DIFFRACTION	8	H	2 - 58
9	X-RAY DIFFRACTION	9	I	2 - 58
10	X-RAY DIFFRACTION	10	J	2 - 58
11	X-RAY DIFFRACTION	11	K	2 - 58
12	X-RAY DIFFRACTION	12	L	2 - 58

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-Aug 12, 2020. Covid-19 info

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+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi