PDB-7ahs: titin-N2A Ig81-Ig83

ID or keywords:

Entry

Database: PDB / ID: 7ahs

Title

titin-N2A Ig81-Ig83

Components

Isoform 5 of Titin

Keywords

STRUCTURAL PROTEIN / Titin / N2A

Function / homology

Function and homology information

sarcomerogenesis / titin-telethonin complex / structural molecule activity conferring elasticity / skeletal muscle myosin thick filament assembly / telethonin binding / detection of muscle stretch / muscle alpha-actinin binding / : / cardiac myofibril assembly / cardiac muscle hypertrophy ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Fleming, J.R. / Mayans, O.

Citation

Journal: J.Gen.Physiol. / Year: 2021
Title: The N2A region of titin has a unique structural configuration.
Authors: Stronczek, C. / Lange, S. / Bullard, B. / Wolniak, S. / Borgeson, E. / Mayans, O. / Fleming, J.R.

History

Deposition	Sep 25, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 24, 2021	Provider: repository / Type: Initial release
Revision 1.1	Apr 21, 2021	Group: Advisory / Database references / Derived calculations Category: citation / citation_author ...citation / citation_author / pdbx_validate_symm_contact / struct_conn Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Jan 31, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim 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.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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Download

PDBx/mmCIF format	7ahs.cif.gz	559.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7ahs.ent.gz	384.7 KB	Display	PDB format
PDBx/mmJSON format	7ahs.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7ahs_validation.pdf.gz	494.2 KB	Display	wwPDB validaton report
Full document	7ahs_full_validation.pdf.gz	507.3 KB	Display
Data in XML	7ahs_validation.xml.gz	51.8 KB	Display
Data in CIF	7ahs_validation.cif.gz	75.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ah/7ahs ftp://data.pdbj.org/pub/pdb/validation_reports/ah/7ahs	HTTPS FTP

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Related structure data

Related structure data	5joeS S: Starting model for refinement
Similar structure data	5zo1-d 4lp5-2 6bg9-d 6efz-d 4nn0-d 3a69-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

5joeS

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	#185 - May 2015 Titin similarity (12) #267 - Mar 2022 Vascular Endothelial Growth Factor (VegF similarity (2) #52 - Apr 2004 Growth Hormone similarity (1) #141 - Sep 2011 O-GlcNAc Transferase similarity (1)

Deposited unit

A: Isoform 5 of Titin

B: Isoform 5 of Titin

C: Isoform 5 of Titin

D: Isoform 5 of Titin

hetero molecules

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

1

A: Isoform 5 of Titin

hetero molecules

defined by author
Evidence: gel filtration
31.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Isoform 5 of Titin

hetero molecules

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

3

C: Isoform 5 of Titin

hetero molecules

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

4

D: Isoform 5 of Titin

hetero molecules

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

Unit cell

Length a, b, c (Å)	85.203, 87.336, 161.583
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1
4	1

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	MET	MET	GLU	GLU	(chain 'A' and (resid 0 through 51 or resid 53 through 270 or resid 301))	A	A	0 - 50	3 - 53
1	2	ILE	ILE	LEU	LEU	(chain 'A' and (resid 0 through 51 or resid 53 through 270 or resid 301))	A	A	53 - 269	56 - 272
1	3	EDO	EDO	EDO	EDO	(chain 'A' and (resid 0 through 51 or resid 53 through 270 or resid 301))	A	E	301
2	4	MET	MET	GLU	GLU	(chain 'B' and ((resid 0 and (name N or name...	B	B	0 - 50	3 - 53
2	5	ILE	ILE	LEU	LEU	(chain 'B' and ((resid 0 and (name N or name...	B	B	53 - 269	56 - 272
2	6	EDO	EDO	EDO	EDO	(chain 'B' and ((resid 0 and (name N or name...	B	J	301
3	7	MET	MET	GLU	GLU	(chain 'C' and (resid 0 through 51 or resid 53 through 270 or resid 301))	C	C	0 - 50	3 - 53
3	8	ILE	ILE	LEU	LEU	(chain 'C' and (resid 0 through 51 or resid 53 through 270 or resid 301))	C	C	53 - 269	56 - 272
3	9	EDO	EDO	EDO	EDO	(chain 'C' and (resid 0 through 51 or resid 53 through 270 or resid 301))	C	W	301
4	10	MET	MET	GLU	GLU	(chain 'D' and ((resid 0 and (name N or name...	D	D	0 - 50	3 - 53
4	11	ILE	ILE	LEU	LEU	(chain 'D' and ((resid 0 and (name N or name...	D	D	53 - 269	56 - 272
4	12	EDO	EDO	EDO	EDO	(chain 'D' and ((resid 0 and (name N or name...	D	CA	301

#1: Protein	Isoform 5 of Titin / Connectin / Rhabdomyosarcoma antigen MU-RMS-40.14 Mass: 31467.428 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TTN / Production host: Escherichia coli (E. coli) References: UniProt: Q8WZ42, non-specific serine/threonine protein kinase
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 910 / 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: 2.39 Å³/Da / Density % sol: 48.5 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 25 % w/v Polyethylene glycol 3,350, 100 mM BIS-TRIS pH 5.5, 200 mM lithium sulfate

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Data collection

Diffraction	Mean temperature: 80 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 21, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.05→45.67 Å / Num. obs: 747399 / % possible obs: 99.97 % / Redundancy: 9.8 % / B_iso Wilson estimate: 36.09 Å² / CC_1/2: 0.998 / Net I/σ(I): 12.3
Reflection shell	Resolution: 2.05→2.123 Å / Num. unique obs: 72724 / CC_1/2: 0.9997

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Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
XSCALE		data reduction
XDS		data scaling
PHASER		phasing
ARP/wARP		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5JOE

5joe

Resolution: 2.05→45.53 Å / SU ML: 0.305 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3504 / Stereochemistry target values: GeoStd + Monomer Library

	R_factor	Num. reflection	% reflection
R_free	0.2351	1840	2.41 %
R_work	0.1833	74490	-
obs	0.1846	76330	99.99 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 51.39 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→45.53 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8804	0	132	910	9846

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0092	9094
X-RAY DIFFRACTION	f_angle_d	1.215	12285
X-RAY DIFFRACTION	f_chiral_restr	0.0621	1352
X-RAY DIFFRACTION	f_plane_restr	0.0083	1584
X-RAY DIFFRACTION	f_dihedral_angle_d	6.9677	6608

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 (%)
2.05-2.11	0.3493	134	0.2951	5682	X-RAY DIFFRACTION	100
2.11-2.17	0.2985	128	0.2779	5633	X-RAY DIFFRACTION	100
2.17-2.24	0.324	126	0.2685	5725	X-RAY DIFFRACTION	100
2.24-2.32	0.3422	128	0.2596	5645	X-RAY DIFFRACTION	99.98
2.32-2.41	0.3079	112	0.2504	5699	X-RAY DIFFRACTION	99.98
2.41-2.52	0.3095	143	0.2363	5686	X-RAY DIFFRACTION	100
2.52-2.65	0.3031	157	0.2266	5694	X-RAY DIFFRACTION	100
2.65-2.82	0.3034	158	0.2137	5666	X-RAY DIFFRACTION	99.97
2.82-3.04	0.2653	128	0.2081	5729	X-RAY DIFFRACTION	99.98
3.04-3.34	0.2345	136	0.1838	5742	X-RAY DIFFRACTION	100
3.34-3.83	0.2249	189	0.1545	5733	X-RAY DIFFRACTION	100
3.83-4.82	0.1623	166	0.1218	5800	X-RAY DIFFRACTION	100
4.82-45.53	0.2001	135	0.1578	6056	X-RAY DIFFRACTION	99.94

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	8.6006718134	0.400356193145	3.51542135467	2.49217124292	-0.243355272947	4.33696246058	0.376189680443	0.284367006886	-0.40481539817	-0.31076774611	0.0974805637365	0.580921141934	0.105235574404	-0.435838950252	-0.321790838473	0.318474326748	0.0678609214526	-0.0572000294686	0.583712362764	0.13688265279	0.483139422641	24.1141149118	59.9006502388	23.7426011673
2	7.86324955254	-2.21338534647	2.10689763549	1.09617273727	-0.59792292891	1.04088955787	0.199701394694	0.0456247236385	-0.372154570948	-0.133636676882	-0.0357504775045	0.0888916104818	0.148286453535	0.00655568616945	-0.165140120224	0.222965375617	-0.0266808487218	-0.0161460052235	0.211923497567	-0.00676312253096	0.209998815796	66.4554768395	50.1783362267	29.6964986416
3	6.28846572067	-0.577455073757	0.268676990979	3.1656775114	-0.507529317183	0.653854100681	-0.110445253101	0.10640385762	-0.438814325037	0.0228898806312	0.0223699901756	-0.318380356906	0.00368374705083	0.130294725195	0.00504637070358	0.315089445954	-0.00581636703595	0.0167802792945	0.323671774971	-0.0272519930078	0.32518940416	109.333063055	44.8038498074	43.3701637809
4	5.64136973997	1.70106368733	0.80193574311	2.7148102539	0.575790250304	2.16531700963	0.113446738269	-0.109242412347	0.234440418743	0.144478339933	-0.165580470499	-0.195645735392	-0.0993025534955	0.311857100227	0.0493801048675	0.288759396187	-0.0257591271472	0.0273962329807	0.256861337418	0.065871858658	0.262175323001	81.8749493222	72.9909069285	31.7438083334
5	6.90367141987	1.45344924817	-2.31682981748	0.195984617935	-0.616985967036	0.180239450124	0.408059920195	-0.71422592741	0.858682222006	0.146592707639	-0.137034319908	0.162476365183	-0.0992104804016	0.120889608736	-0.328034486499	0.390096445303	-0.0904801089405	0.090724648496	0.474048043183	-0.082266367126	0.437487194778	40.8002439832	67.2601155366	44.4841929175
6	8.33842195692	1.19801328081	1.71748811316	2.28157526315	0.443807922817	2.06478234688	-0.0376565273108	-0.0514304518196	0.14729140728	-0.0762495811916	0.0325588431243	0.148928195198	-0.16182247339	-0.0489881417178	0.00491420612014	0.308631142873	0.010237467567	-0.0072317468457	0.27140753764	-0.00915509484014	0.20881057609	-0.910323424046	59.0482968609	48.3476509238
7	3.34992721714	-1.06067676567	-0.0388778297539	5.42343337268	1.2044117253	3.80137781427	-0.0596739322355	0.193568617328	0.0991919609645	-0.511512094778	-0.0369334682191	0.30090480442	-0.73525923451	-0.480932901684	0.0524437468662	0.452956393737	0.0417292523857	-0.00452416244539	0.401502704442	0.0137573546015	0.226637569207	85.0105599744	83.3970055462	-8.63137080483
8	-0.594195941116	0.567170154456	0.052378146913	7.27207375735	-2.62432906801	0.291608406375	-0.161886102092	0.0445215551994	0.0518772185341	0.342895331643	0.622269478635	0.978378396036	-0.0248779505699	-0.199458547468	-0.457765847893	0.534081125479	-0.00912296762874	0.0489897476725	0.421008079242	0.105687694435	0.584994761226	86.464872513	42.1508466325	3.74861239485
9	2.0267141922	-1.07229679384	-0.0326621264855	5.0336251977	-0.223070908135	2.32286706077	0.0765422282251	0.190706191699	0.0584191501583	-0.366843506785	-0.16181104992	-0.0830522862927	-0.199511534577	-0.0119870415049	0.0911623227526	0.246187474193	-0.00980949540223	0.0438021685797	0.282387142681	0.0204263182407	0.193800469432	91.3288694908	0.120216962429	12.0897616041
10	3.27552313345	-3.50923498146	-0.492489267036	6.08677204818	0.320433988472	1.93831998678	0.410517681918	0.0824000638723	0.0233330760864	-2.17170641246	0.0311796526617	-0.47009511234	0.233352406034	0.248152762623	-0.339691587485	1.11966536374	-0.0224338990086	0.163648547181	0.452569299943	-0.0165095850648	0.512059563851	103.648217475	26.2376297991	-11.3082672539
11	0.335307325806	-0.36080934882	-0.206166529955	6.86411462082	1.86537645183	1.07123458117	-0.100837688067	0.0691040144759	-0.0582500201889	-0.0308138735199	0.264661842305	-0.806422189369	-0.0508784682526	0.174219432231	-0.198552888581	0.290644235097	-0.0269341539177	0.096638220742	0.366720140857	-0.0310611835041	0.521261292606	107.75337141	68.9819162659	-1.22479750912
12	1.0832604818	0.180238851953	0.486004953059	7.60282462556	-1.29962106641	0.451139822686	0.33259676025	-0.14587171343	1.3890635517	0.28085322149	-0.102755263731	-0.674228748799	-0.775471889162	0.29599849874	-0.207685687358	0.807288676466	-0.0650819922953	0.222316686308	0.50823336844	-0.0138362074182	1.21860362291	106.807573154	113.312026034	12.2064983648

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 79 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 80 through 188 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 189 through 270 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid -1 through 79 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 80 through 188 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 189 through 270 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 0 through 79 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 80 through 188 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 189 through 270 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid -1 through 79 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 80 through 188)
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 189 through 227)

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Yorodumi