PDB-8udn: A Stable Heterotrimeric Foldon with Minimum Mutation

ID or keywords:

Entry

Database: PDB / ID: 8udn

Title

A Stable Heterotrimeric Foldon with Minimum Mutation

Components

Fibritin

Keywords

VIRAL PROTEIN / Foldon Heterotrimer Self-assembly Peptides Miniprotein

Function / homology

Fibritin C-terminal / Fibritin C-terminal region / virion component / Fibritin

Function and homology information

Biological species

Tequatrovirus T4

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 0.97 Å

Authors

Bingman, C.A. / Liu, X. / Roberts, D.S. / Gellman, S.H.

Funding support

United States, 1items

Citation

Journal: J.Am.Chem.Soc. / Year: 2025
Title: Rational Design of a Foldon-Derived Heterotrimer Guided by Quantitative Native Mass Spectrometry.
Authors: Liu, X. / Roberts, D.S. / Bingman, C.A. / Ge, Y. / Gellman, S.H.

History

Deposition	Sep 28, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 14, 2025	Provider: repository / Type: Initial release
Revision 1.1	Jul 9, 2025	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2	Jul 16, 2025	Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3	Jul 23, 2025	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8udn.cif.gz	143.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8udn.ent.gz	123.3 KB	Display	PDB format
PDBx/mmJSON format	8udn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8udn_validation.pdf.gz	432.2 KB	Display	wwPDB validaton report
Full document	8udn_full_validation.pdf.gz	434.4 KB	Display
Data in XML	8udn_validation.xml.gz	10.7 KB	Display
Data in CIF	8udn_validation.cif.gz	17.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ud/8udn ftp://data.pdbj.org/pub/pdb/validation_reports/ud/8udn	HTTPS FTP

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Related structure data

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	#170 - Feb 2014 Broadly Neutralizing Antibodies similarity (3) #246 - Jun 2020 SARS-CoV-2 Spike similarity (2)

Deposited unit

A: Fibritin

B: Fibritin

C: Fibritin

9.39 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	32.854, 32.854, 75.230
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	78
Space group name H-M	P4₃

#1: Protein/peptide	Fibritin / Collar protein / Whisker antigen control protein Mass: 3129.521 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tequatrovirus T4 / Gene: wac / Production host: synthetic construct (others) / References: UniProt: P10104
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.14 Å³/Da / Density % sol: 42.61 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / Details: MPD

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-B / Wavelength: 0.6199 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2022

Radiation

Monochromator: Si(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.6199 Å / Relative weight: 1

Reflection

Resolution: 0.97→30.11 Å / Num. obs: 46727 / % possible obs: 99 % / Redundancy: 14 % / CC_1/2: 1 / R_merge(I) obs: 0.058 / R_rim(I) all: 0.06 / Net I/σ(I): 17.4

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID	% possible all
0.97-0.99	1.274	3444	0.759	1.32	1	98.3
0.99-1.02	0.981	3314	0.836	1.018	1	98.5
1.02-1.05	0.745	3296	0.888	0.774	1	98.7
1.05-1.08	0.537	3121	0.934	0.558	1	98.8
1.08-1.12	0.42	3077	0.961	0.437	1	99
1.12-1.16	0.348	2947	0.971	0.361	1	97.5
1.16-1.2	0.296	2854	0.983	0.306	1	99.3
1.2-1.25	0.269	2792	0.985	0.279	1	99.3
1.25-1.31	0.238	2671	0.987	0.247	1	99.4
1.31-1.37	0.215	2549	0.989	0.223	1	99.5
1.37-1.44	0.176	2442	0.992	0.182	1	99.7
1.44-1.53	0.139	2277	0.995	0.145	1	99.6
1.53-1.64	0.111	2141	0.996	0.116	1	97.9
1.64-1.77	0.087	2001	0.998	0.09	1	99.9
1.77-1.94	0.064	1888	0.999	0.066	1	99.8
1.94-2.17	0.05	1660	0.999	0.052	1	99.8
2.17-2.5	0.04	1497	0.999	0.041	1	100
2.5-3.06	0.033	1227	1	0.034	1	97.5
3.06-4.33	0.026	973	1	0.026	1	99.5
4.33-30.11	0.024	556	0.999	0.025	1	98.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XDS	Jan 10, 2022 BUILT=20220220	data scaling
XDS	Jan 10, 2022 BUILT=20220220	data reduction
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 0.97→22.2 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.35 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1575	2006	4.3 %	thin shells
R_work	0.1454	-	-	-
obs	0.1459	46689	99.03 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 0.97→22.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	690	0	0	117	807

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	2061
X-RAY DIFFRACTION	f_angle_d	1.093	2793
X-RAY DIFFRACTION	f_dihedral_angle_d	13.691	771
X-RAY DIFFRACTION	f_chiral_restr	0.075	282
X-RAY DIFFRACTION	f_plane_restr	0.012	360

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 (%)
0.97-0.99	0.3131	106	0.2784	3209	X-RAY DIFFRACTION	98
0.99-1.02	0.2656	200	0.2397	3105	X-RAY DIFFRACTION	99
1.02-1.05	0.23	101	0.2059	3210	X-RAY DIFFRACTION	99
1.05-1.08	0.176	207	0.1729	3091	X-RAY DIFFRACTION	99
1.08-1.12	0.161	103	0.1547	3223	X-RAY DIFFRACTION	99
1.12-1.17	0.1494	102	0.1467	3203	X-RAY DIFFRACTION	98
1.17-1.22	0.1537	197	0.1343	3178	X-RAY DIFFRACTION	99
1.22-1.29	0.1584	105	0.1398	3186	X-RAY DIFFRACTION	99
1.29-1.37	0.1716	200	0.1315	3175	X-RAY DIFFRACTION	100
1.37-1.47	0.133	101	0.1398	3238	X-RAY DIFFRACTION	100
1.47-1.62	0.1577	100	0.1445	3215	X-RAY DIFFRACTION	99
1.62-1.85	0.1502	199	0.1366	3177	X-RAY DIFFRACTION	100
1.85-2.33	0.1428	97	0.1357	3289	X-RAY DIFFRACTION	100
2.34-22.2	0.1525	188	0.1432	3184	X-RAY DIFFRACTION	99

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	7.9065	-0.9431	-1.7666	1.6612	-0.178	2.3732	-0.0154	0.1077	-0.4022	-0.0088	0.0291	0.0502	0.2251	0.0369	-0.0029	0.0738	0.0007	-0.0081	0.0623	0.0126	0.0854	17.3397	-9.2798	1.9131
2	6.1928	-1.4424	1.2408	1.9128	0.8847	5.1967	-0.0184	0.0387	-0.0248	-0.2573	0.0805	-0.1349	0.1236	0.2642	-0.0558	0.065	0.0091	0.0078	0.0268	0.0012	0.0827	18.7484	-5.0429	-7.0354
3	1.3144	0.7952	-0.133	2.6385	-2.72	3.6394	-0.0116	-0.0381	0.0253	0.028	0.1073	0.1978	-0.1921	-0.252	-0.1224	0.0424	0.0088	-0.0004	0.0577	-0.0012	0.1033	8.1528	-3.306	-2.4798
4	0.5982	0.9045	0.5565	3.9787	-0.6588	4.1274	-0.0209	0.0048	0.0708	0.1775	0.0358	0.0775	-0.1251	-0.01	0.0154	0.041	0.0206	-0.0015	0.0268	-0.0014	0.0832	13.6653	5.3955	-3.7385
5	2.6871	1.529	-0.1489	4.9698	-0.1212	1.2938	-0.0434	-0.1376	0.0373	0.696	0.1034	0.089	-0.1981	-0.0597	-0.0607	0.1503	0.0261	0.0079	0.079	0.0008	0.0828	14.0737	1.2377	6.6984
6	1.9563	-1.6608	1.6506	7.7824	0.4268	2.2685	-0.2413	0.0536	0.2517	0.1469	-0.0347	-0.4467	-0.3315	0.2774	0.1995	0.0719	-0.0115	-0.0284	0.0856	0.0203	0.1101	23.031	1.172	2.4217

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 12 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 13 through 27 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 1 through 12 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 13 through 27 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 1 through 12 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 13 through 27 )

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