PDB-4ltb: Coiled-coil domain of TRIM25

Basic information

• Entry: Database: PDB / ID: 4ltb
• Title: Coiled-coil domain of TRIM25
• Components: Tripartite motif-containing 25 variant
• Keywords: METAL BINDING PROTEIN / Coiled-coil

Function / homology

Function:

: / RIG-I binding / regulation of viral entry into host cell / suppression of viral release by host / negative regulation of viral entry into host cell / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / response to vitamin D / ERAD pathway / TRAF6 mediated IRF7 activation / cytoplasmic pattern recognition receptor signaling pathway / protein monoubiquitination / antiviral innate immune response / TRAF6 mediated NF-kB activation / ligase activity / viral release from host cell / protein K48-linked ubiquitination / cellular response to leukemia inhibitory factor / Negative regulators of DDX58/IFIH1 signaling / Termination of translesion DNA synthesis / DDX58/IFIH1-mediated induction of interferon-alpha/beta / RING-type E3 ubiquitin transferase / PKR-mediated signaling / ISG15 antiviral mechanism / cytoplasmic stress granule / response to estrogen / ubiquitin-protein transferase activity / SARS-CoV-1 activates/modulates innate immune responses / regulation of protein localization / ubiquitin protein ligase activity / positive regulation of DNA-binding transcription factor activity / Interferon gamma signaling / Ovarian tumor domain proteases / TRAF3-dependent IRF activation pathway / positive regulation of NF-kappaB transcription factor activity / ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / response to oxidative stress / transcription coactivator activity / nuclear body / cadherin binding / innate immune response / SARS-CoV-2 activates/modulates innate and adaptive immune responses / RNA binding / nucleoplasm / metal ion binding / cytosol / cytoplasm

Domain/homology:

TRIM25, PRY/SPRY domain / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type

Component:

E3 ubiquitin/ISG15 ligase TRIM25 / Tripartite motif-containing 25 variant

• Biological species: Homo sapiens (human)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
• Authors: Pornillos, O. / Sanchez, J.G. / Okreglicka, K.
• Citation: Journal: Proc.Natl.Acad.Sci.USA / Year: 2014; Title: The tripartite motif coiled-coil is an elongated antiparallel hairpin dimer.; Authors: Sanchez, J.G. / Okreglicka, K. / Chandrasekaran, V. / Welker, J.M. / Sundquist, W.I. / Pornillos, O.

History

Deposition	Jul 23, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 5, 2014	Provider: repository / Type: Initial release
Revision 1.1	Mar 19, 2014	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Assembly

Deposited unit

A: Tripartite motif-containing 25 variant

B: Tripartite motif-containing 25 variant

Summary:

• 43.7 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	43,744	2
Polymers	43,744	2
Non-polymers	0	0
Water	991	55

1

Summary:

• Idetical with deposited unit
• defined by author&software

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	10540 Å2
ΔGint	-81 kcal/mol
Surface area	20770 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	57.669, 83.158, 92.851
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P212121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
1	2
2	2
1	3
2	3
1	4
2	4
1	5
2	5
1	6
2	6
1	7
2	7
1	8
2	8
1	9
2	9
1	10
2	10
1	11
2	11
1	12
2	12
1	13
2	13
1	14
2	14
1	15
2	15
1	16
2	16

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	chain 'B' and (resseq 190:192 or (resseq 193 and backbone)...
2	1	1	chain 'A' and (resseq 190:192 or (resseq 193 and backbone)...
1	1	2	chain 'B' and (resseq 202:208 )
2	1	2	chain 'A' and (resseq 202:208 )
1	1	3	chain 'B' and (resseq 209:215 )
2	1	3	chain 'A' and (resseq 209:215 )
1	1	4	chain 'B' and (resseq 216:217 or (resseq 218 and backbone) or resseq 219:222 )
2	1	4	chain 'A' and (resseq 216:217 or (resseq 218 and backbone) or resseq 219:222 )
1	1	5	chain 'B' and (resseq 223:225 or (resseq 226 and backbone)...
2	1	5	chain 'A' and (resseq 223:225 or (resseq 226 and backbone)...
1	1	6	chain 'B' and (resseq 234:235 or (resseq 236 and backbone...
2	1	6	chain 'A' and (resseq 234:235 or (resseq 236 and backbone...
1	1	7	chain 'B' and (resseq 245:251 )
2	1	7	chain 'A' and (resseq 245:251 )
1	1	8	chain 'B' and (resseq 252:260 or (resseq 261 and backbone) or resseq 262 )
2	1	8	chain 'A' and (resseq 252:260 or (resseq 261 and backbone) or resseq 262 )
1	1	9	chain 'B' and (resseq 263:267 or (resseq 268 and backbone) or resseq 269:273 )
2	1	9	chain 'A' and (resseq 263:267 or (resseq 268 and backbone) or resseq 269:273 )
1	1	10	chain 'B' and (resseq 274:280 )
2	1	10	chain 'A' and (resseq 274:280 )
1	1	11	chain 'B' and (resseq 281:282 or (resseq 283:284 and backbone)...
2	1	11	chain 'A' and (resseq 281:282 or (resseq 283:284 and backbone)...
1	1	12	chain 'B' and (resseq 288:298 )
2	1	12	chain 'A' and (resseq 288:298 )
1	1	13	chain 'B' and (resseq 329:330 or (resseq 331:332 and backbone)...
2	1	13	chain 'A' and (resseq 329:330 or (resseq 331:332 and backbone)...
1	1	14	chain 'B' and (resseq 337:347 )
2	1	14	chain 'A' and (resseq 337:347 )
1	1	15	chain 'B' and (resseq 348:353 or (resseq 354 and backbone) or resseq 355:356 )
2	1	15	chain 'A' and (resseq 348:353 or (resseq 354 and backbone) or resseq 355:356 )
1	1	16	chain 'B' and ((resseq 306:307 and backbone) or resseq 308:314 or (resseq 315 and backbone) )
2	1	16	chain 'A' and (resseq 306:315 )

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16

• Details: asymmetric unit

Components

#1: Protein

A B Tripartite motif-containing 25 variant

Details:

Mass: 21871.787 Da / Num. of mol.: 2 / Fragment: Coiled-coil/L2 fragment residues 203-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q59GW5, UniProt: Q14258*PLUS

#2: Water

ChemComp-HOH / water / Water

Details:

Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION

Sample preparation

• Crystal: Density Matthews: 2.54 ų/Da / Density % sol: 51.67 %
• Crystal grow: Temperature: 290 K / Method: vapor diffusion, sitting drop; Details: 6-12% PEG 4000, 10 mM sodium acetate, pH 5.3-6.6, VAPOR DIFFUSION, SITTING DROP, temperature 290K; PH range: 5.3-6.6

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
• Detector: Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 8, 2013
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 1 Å / Relative weight: 1
• Reflection: Resolution: 2.6→50 Å / Num. obs: 13941 / % possible obs: 96.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.1 % / B_iso Wilson estimate: 43.8 Ų / R_sym value: 0.14 / Net I/σ(I): 17.3
• Reflection shell: Resolution: 2.6→2.69 Å / Redundancy: 9.1 % / Mean I/σ(I) obs: 2.2 / R_sym value: 0.78 / % possible all: 81.4

Processing

Software

Name	Version	Classification
PHENIX	(AutoMR)	model building
PHENIX	(phenix.refine: dev_1427)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX	(AutoMR)	phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→42.209 Å / SU ML: 0.33 / σ(F): 0 / Phase error: 29.44 / Stereochemistry target values: ML

	Rfactor	Num. reflection	% reflection
Rfree	0.2572	1296	9.94 %
Rwork	0.2028	-	-
obs	0.2082	13042	90.33 %

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

Refinement step

Cycle: LAST / Resolution: 2.59→42.209 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2778	0	0	55	2833

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	2802
X-RAY DIFFRACTION	f_angle_d	1.165	3752
X-RAY DIFFRACTION	f_dihedral_angle_d	15.321	1130
X-RAY DIFFRACTION	f_chiral_restr	0.076	438
X-RAY DIFFRACTION	f_plane_restr	0.004	480

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	B	73	X-RAY DIFFRACTION	POSITIONAL
1	2	A	73	X-RAY DIFFRACTION	POSITIONAL	0.033
2	1	B	60	X-RAY DIFFRACTION	POSITIONAL
2	2	A	60	X-RAY DIFFRACTION	POSITIONAL	0.043
3	1	B	55	X-RAY DIFFRACTION	POSITIONAL
3	2	A	55	X-RAY DIFFRACTION	POSITIONAL	0.048
4	1	B	44	X-RAY DIFFRACTION	POSITIONAL
4	2	A	44	X-RAY DIFFRACTION	POSITIONAL	0.051
5	1	B	73	X-RAY DIFFRACTION	POSITIONAL
5	2	A	73	X-RAY DIFFRACTION	POSITIONAL	0.065
6	1	B	81	X-RAY DIFFRACTION	POSITIONAL
6	2	A	81	X-RAY DIFFRACTION	POSITIONAL	0.035
7	1	B	58	X-RAY DIFFRACTION	POSITIONAL
7	2	A	58	X-RAY DIFFRACTION	POSITIONAL	0.033
8	1	B	76	X-RAY DIFFRACTION	POSITIONAL
8	2	A	76	X-RAY DIFFRACTION	POSITIONAL	0.039
9	1	B	89	X-RAY DIFFRACTION	POSITIONAL
9	2	A	89	X-RAY DIFFRACTION	POSITIONAL	0.039
10	1	B	63	X-RAY DIFFRACTION	POSITIONAL
10	2	A	63	X-RAY DIFFRACTION	POSITIONAL	0.041
11	1	B	43	X-RAY DIFFRACTION	POSITIONAL
11	2	A	43	X-RAY DIFFRACTION	POSITIONAL	0.052
12	1	B	91	X-RAY DIFFRACTION	POSITIONAL
12	2	A	91	X-RAY DIFFRACTION	POSITIONAL	0.039
13	1	B	48	X-RAY DIFFRACTION	POSITIONAL
13	2	A	48	X-RAY DIFFRACTION	POSITIONAL	0.032
14	1	B	90	X-RAY DIFFRACTION	POSITIONAL
14	2	A	90	X-RAY DIFFRACTION	POSITIONAL	0.034
15	1	B	65	X-RAY DIFFRACTION	POSITIONAL
15	2	A	65	X-RAY DIFFRACTION	POSITIONAL	0.038
16	1	B	66	X-RAY DIFFRACTION	POSITIONAL
16	2	A	66	X-RAY DIFFRACTION	POSITIONAL	0.045

LS refinement shell

Resolution (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	Refine-ID	% reflection obs (%)
2.5896-2.6932	0.3643	94	0.3	892	X-RAY DIFFRACTION	63
2.6932-2.8158	0.3646	120	0.2988	1083	X-RAY DIFFRACTION	76
2.8158-2.9642	0.3586	136	0.2686	1230	X-RAY DIFFRACTION	86
2.9642-3.1499	0.314	142	0.229	1309	X-RAY DIFFRACTION	92
3.1499-3.393	0.2839	155	0.2189	1392	X-RAY DIFFRACTION	97
3.393-3.7342	0.2424	155	0.196	1402	X-RAY DIFFRACTION	98
3.7342-4.2741	0.2543	159	0.1757	1431	X-RAY DIFFRACTION	99
4.2741-5.3832	0.1958	162	0.1833	1460	X-RAY DIFFRACTION	100
5.3832-42.2148	0.2327	173	0.178	1547	X-RAY DIFFRACTION	100