PDB-6d02: Cross-alpha Amyloid-like Structure alphaAmL, 2nd form

ID or keywords:

Entry

Database: PDB / ID: 6d02

Title

Cross-alpha Amyloid-like Structure alphaAmL, 2nd form

Components

alpha-Amyloid peptide alphaAmL

Keywords

DE NOVO PROTEIN / alpha-amyloid / protein desidn / de Novo / coiled-coil / fabril

Function / homology

CARBONATE ION / PHOSPHATE ION

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Zhang, S.-Q. / Liu, L. / Degrado, W.F.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R35GM122603	United States
National Science Foundation (NSF, United States)	CHE1413295	United States

Citation

Journal: Nat. Chem. Biol. / Year: 2018
Title: Designed peptides that assemble into cross-alpha amyloid-like structures.
Authors: Zhang, S.Q. / Huang, H. / Yang, J. / Kratochvil, H.T. / Lolicato, M. / Liu, Y. / Shu, X. / Liu, L. / DeGrado, W.F.

History

Deposition	Apr 10, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 20, 2019	Provider: repository / Type: Initial release
Revision 1.1	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Oct 4, 2023	Group: 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6d02.cif.gz	306.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6d02.ent.gz	257.3 KB	Display	PDB format
PDBx/mmJSON format	6d02.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6d02_validation.pdf.gz	617.1 KB	Display	wwPDB validaton report
Full document	6d02_full_validation.pdf.gz	623.2 KB	Display
Data in XML	6d02_validation.xml.gz	26.6 KB	Display
Data in CIF	6d02_validation.cif.gz	39 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d0/6d02 ftp://data.pdbj.org/pub/pdb/validation_reports/d0/6d02	HTTPS FTP

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Related structure data

Related structure data	6c4xC 6c4yC 6c4zC 6c50C 6c51SC 6c52C 6o3nC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2qr5-d 3wmt-d 3c5j-2 5odn-d 1z9o-d 4ga5-2 2hu8-d 5zum-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#70 - Oct 2005 Designer Proteins similarity (1) #193 - Jan 2016 Siderocalin similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #35 - Nov 2002 Ferritin and Transferrin similarity (1) #37 - Jan 2003 Serum Albumin similarity (1)

Deposited unit

A: alpha-Amyloid peptide alphaAmL

B: alpha-Amyloid peptide alphaAmL

C: alpha-Amyloid peptide alphaAmL

D: alpha-Amyloid peptide alphaAmL

E: alpha-Amyloid peptide alphaAmL

F: alpha-Amyloid peptide alphaAmL

G: alpha-Amyloid peptide alphaAmL

H: alpha-Amyloid peptide alphaAmL

I: alpha-Amyloid peptide alphaAmL

J: alpha-Amyloid peptide alphaAmL

K: alpha-Amyloid peptide alphaAmL

L: alpha-Amyloid peptide alphaAmL

M: alpha-Amyloid peptide alphaAmL

N: alpha-Amyloid peptide alphaAmL

O: alpha-Amyloid peptide alphaAmL

P: alpha-Amyloid peptide alphaAmL

Q: alpha-Amyloid peptide alphaAmL

R: alpha-Amyloid peptide alphaAmL

S: alpha-Amyloid peptide alphaAmL

T: alpha-Amyloid peptide alphaAmL

U: alpha-Amyloid peptide alphaAmL

V: alpha-Amyloid peptide alphaAmL

W: alpha-Amyloid peptide alphaAmL

X: alpha-Amyloid peptide alphaAmL

Y: alpha-Amyloid peptide alphaAmL

Z: alpha-Amyloid peptide alphaAmL

a: alpha-Amyloid peptide alphaAmL

b: alpha-Amyloid peptide alphaAmL

c: alpha-Amyloid peptide alphaAmL

d: alpha-Amyloid peptide alphaAmL

e: alpha-Amyloid peptide alphaAmL

f: alpha-Amyloid peptide alphaAmL

hetero molecules

95.7 kDa, 32 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: scanning transmission electron microscopy

Unit cell

Length a, b, c (Å)	107.546, 107.777, 99.374
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein/peptide	... alpha-Amyloid peptide alphaAmL Mass: 2974.649 Da / Num. of mol.: 32 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Formula: PO₄
#4: Chemical	ChemComp-CO3 / CARBONATE ION Mass: 60.009 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Formula: CO₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.12 Å³/Da / Density % sol: 60.56 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 45% MPD, 0.6 M NaH2PO4

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 8, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 2.5→108 Å / Num. obs: 41301 / % possible obs: 100 % / Redundancy: 10.9 % / Net I/σ(I): 16.5
Reflection shell	Resolution: 2.5→2.59 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4048 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6C51 generated antiparallel bundle

6c51

Resolution: 2.5→19.977 Å / Cross valid method: FREE R-VALUE / σ(F): 68.01 / Phase error: 26.1

	R_factor	Num. reflection	% reflection
R_free	0.2773	1006	2.48 %
R_work	0.2324	-	-
obs	0.2383	40529	99.97 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.5→19.977 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5927	0	27	124	6078

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	6002
X-RAY DIFFRACTION	f_angle_d	1.122	8078
X-RAY DIFFRACTION	f_dihedral_angle_d	28.64	2127
X-RAY DIFFRACTION	f_chiral_restr	0.044	1057
X-RAY DIFFRACTION	f_plane_restr	0.005	901

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 (%)
2.5001-2.6316	0.3022	144	0.2695	5556	X-RAY DIFFRACTION	97
2.6316-2.7961	0.2931	140	0.2619	5557	X-RAY DIFFRACTION	98
2.7961-3.0113	0.2709	151	0.2486	5580	X-RAY DIFFRACTION	97
3.0113-3.3131	0.2633	144	0.2288	5604	X-RAY DIFFRACTION	97
3.3131-3.7897	0.25	151	0.2335	5615	X-RAY DIFFRACTION	97
3.7897-4.7639	0.2628	129	0.2206	5708	X-RAY DIFFRACTION	98
4.7639-19.9773	0.3213	145	0.2377	5902	X-RAY DIFFRACTION	98

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	1.9202	-1.6396	-1.9245	5.4846	4.6052	4.0989	0.7322	0.0484	0.0233	-0.9171	-0.1135	0.0139	-0.7009	-0.3503	-0.3537	0.6629	-0.1664	-0.101	0.7271	0.1202	0.2568	102.1	133.3864	140.5442
2	0.8065	0.6631	-0.4876	1.1346	-1.2658	3.7282	-0.0905	0.1953	0.0423	-0.3918	0.3822	0.0277	0.4327	0.3076	-0.1601	0.5206	-0.2127	-0.0159	1.2879	0.1411	0.3159	94.4933	124.5802	138.1387
3	0.2724	0.2317	0.2877	0.4111	-0.1814	1.1116	-0.0193	0.1988	-0.0032	-0.2262	0.1355	0.0552	0.3359	-0.1358	0.2212	0.4188	0.1001	0.1666	0.7223	0.1753	0.08	102.0307	132.1694	129.2887
4	0.5179	0.8386	0.3728	2.8041	1.5478	3.2144	-0.0574	-0.0988	0.1195	-0.2487	-0.19	0.1171	0.0887	-0.0447	0.1084	0.2972	-0.0453	0.0085	1.2533	0.0201	0.2013	92.1685	134.7055	131.3757
5	3.5536	0.5171	1.1937	0.9232	0.0764	2.4052	-0.0278	-0.2598	0.0623	0.4802	0.0143	0.045	-0.1935	-0.0168	0.0545	0.5193	0.0784	0.0696	0.5058	0.1006	0.0622	109.9505	143.6758	129.167
6	3.2004	0.6169	-0.0108	0.9969	-0.9443	4.4308	-0.4793	0.0587	0.2331	-0.2132	0.1323	0.1623	-0.4368	-0.4516	0.2178	0.9306	0.2981	-0.0091	0.4543	-0.0119	0.1847	102.3001	152.0209	126.3673
7	1.1223	-0.3088	-0.0858	0.8633	-0.1097	0.4511	0.1326	0.0813	-0.0183	-0.3484	-0.1682	0.0681	-0.2635	-0.1329	-0.1215	0.4114	-0.1692	-0.0327	0.5033	-0.0661	-0.1486	108.6245	143.0894	117.5576
8	2.0917	-0.3192	1.6188	0.479	-0.1207	5.0557	-0.156	0.2649	0.0386	0.0119	-0.1312	-0.0785	-0.1667	0.358	-0.0199	1.0415	-0.0484	0.2002	0.2898	-0.0347	0.201	112.4535	152.5003	119.5367
9	1.2099	0.6212	-0.9594	3.2592	-0.3201	4.2154	0.0258	-0.3162	-0.056	0.0052	0.1064	-0.1412	0.0868	0.5253	0.0179	0.2164	-0.1688	0.0323	0.4999	-0.0502	0.1392	118.7893	134.8923	117.0274
10	1.7704	-1.3846	1.8607	3.3132	-2.1688	3.9155	-0.2642	-0.152	0.2566	0.2369	-0.1635	-0.45	-0.6003	0.4481	0.3291	0.3483	-0.2169	-0.0102	0.9694	-0.1048	0.2542	127.0506	141.477	114.3515
11	0.7077	0.1825	-0.455	1.7975	-0.9885	1.8008	-0.0464	0.1893	0.1248	-0.0397	0.1426	0.0063	-0.12	0.1185	0.1624	0.2893	0.0652	-0.0751	0.2556	0.0852	-0.1159	118.7749	136.3751	105.4519
12	0.6172	0.2864	0.8793	1.1186	-0.1522	2.5125	-0.0498	0.0535	-0.0415	-0.0571	-0.0037	-0.0354	-0.0073	0.1271	-0.1261	0.2068	0.0087	-0.0049	1.0464	-0.0628	0.1105	128.1457	131.8654	108.1755
13	2.1341	-0.3255	1.3871	2.1668	-0.0012	3.2254	0.0222	-0.0469	-0.0451	0.1725	-0.1173	0.0534	0.1556	0.0514	-0.0722	0.1468	0.0465	-0.0976	0.3056	0.041	0.0794	108.9175	126.1118	105.4669
14	1.1054	0.0183	0.8554	1.0625	-0.6999	3.3441	-0.194	-0.0117	0.0327	0.1272	-0.1928	-0.145	0.3653	0.4012	0.2593	1.0612	0.1049	-0.0157	0.3129	-0.0016	0.2248	115.1527	117.4033	102.5021
15	1.3503	-0.0238	0.0154	1.4139	-0.0503	2.0316	0.0805	0.0005	-0.0166	-0.2754	-0.051	-0.0968	0.1673	0.0368	0.0273	0.2786	0.0155	0.0027	0.3597	0.0588	-0.0934	109.9712	126.2583	93.7581
16	3.1808	0.4097	-1.4263	1.7312	-1.2268	1.735	-0.1684	-0.0808	-0.1223	0.1171	-0.1553	0.007	0.0241	0.1926	-0.2973	1.228	-0.0826	0.0103	0.1683	0.0842	0.2345	105.751	116.9431	95.9108
17	1.4787	0.0457	0.0094	3.8284	2.048	4.034	-0.1868	-0.2401	0.0235	0.1013	0.2046	-0.0185	-0.2631	-0.2039	-0.0111	0.3355	-0.0877	-0.0707	0.3946	0.051	0.0033	101.4982	136.4148	93.2532
18	3.6296	-0.7955	-0.39	3.7513	0.7275	0.324	-0.018	0.0214	-0.3709	0.0293	-0.0855	0.4999	0.0459	-0.1734	0.1389	0.1238	-0.0231	0.0056	0.8795	0.1086	0.2473	91.7577	130.8027	90.6748
19	0.8892	0.531	-0.0955	3.6247	0.8257	1.2542	-0.0931	0.3705	0.0392	-0.2653	0.2232	0.0414	0.2244	-0.2756	-0.0449	0.3649	0.1072	0.0338	0.5098	0.0246	0.0579	101.5304	134.5777	81.9169
20	0.2034	0.4337	-0.0761	3.9524	-0.1416	4.6224	-0.0184	-0.1917	0.0878	0.0036	-0.0215	-0.0009	-0.3334	-0.0146	0.0075	0.2586	0.1203	0.0337	1.076	0.0969	0.1771	92.467	140.941	84.2683
21	3.4219	-0.0755	2.4643	0.9407	0.0827	3.214	0.1568	-0.1734	-0.0917	0.4199	-0.0643	-0.1043	0.0102	0.1813	-0.0313	0.4951	-0.0186	0.0066	0.416	-0.0195	0.0658	111.409	142.8261	81.1105
22	0.904	0.365	0.2292	1.0365	0.3026	0.1573	-0.1253	0.0236	0.1577	0.0226	-0.056	0.1979	-0.241	0.0411	-0.2717	1.1852	-0.109	-0.1194	0.2272	0.0245	0.2807	107.3764	152.6159	78.8483
23	2.0504	-0.2783	1.1007	0.6568	-0.1907	1.5307	0.0086	0.0521	0.032	-0.1589	0.0093	0.0082	-0.1875	-0.1005	-0.0303	0.4189	-0.0311	0.0227	0.3522	-0.0293	-0.0692	110.0316	143.1613	69.7296
24	3.0773	-0.9441	-2.3841	0.8352	1.1857	4.4289	0.0155	-0.1883	-0.0059	0.3687	-0.0335	-0.0628	0.0863	0.6227	-0.0514	1.1391	-0.2491	0.0762	0.4345	-0.0466	0.132	116.9345	151.6919	72.1846
25	0.9194	0.0456	0.0592	1.1068	0.0812	1.5534	-0.1663	-0.1572	-0.135	0.1739	0.0203	-0.0058	0.1593	-0.0762	-0.1836	0.4301	0.0488	0.0414	0.592	0.2102	0.0147	118.5559	132.2534	69.3963
26	0.816	-0.3308	-0.1859	1.3279	-0.1265	0.776	-0.0658	-0.1838	-0.0056	0.0375	-0.1758	-0.0256	0.091	0.3311	-0.2225	0.275	0.0827	0.0118	1.2657	-0.0499	0.2144	128.1674	135.6353	67.0185
27	2.7376	1.1982	0.1768	5.1275	-3.0099	6.1912	0.0252	0.4167	-0.1102	-0.1026	0.3027	0.178	-0.3717	0.1702	-0.2951	0.5391	0.2518	-0.0252	0.4196	-0.0419	0.1433	118.4903	134.0342	57.4549
28	0.6976	-0.5555	0.3442	0.6855	0.2591	1.3415	-0.2214	-0.3236	-0.0592	0.4768	0.192	-0.1636	0.2195	-0.039	-0.2334	0.4493	0.2569	-0.0846	1.2729	-0.003	0.2973	126.6042	126.4006	60.3359
29	1.67	-0.4978	0.1788	1.2395	0.5147	0.3144	0.0346	-0.0541	-0.0009	-0.0139	-0.2263	0.0696	0.1207	-0.0106	0.0921	0.5277	-0.0189	-0.0293	0.5234	0.0419	0.0711	108.5252	126.401	56.7224
30	8.7536	-1.0321	-1.0687	0.6372	0.1631	1.3541	0.0103	-0.8005	-0.1973	-0.2936	-0.074	-0.1604	0.5818	-0.1536	0.0785	1.1079	0.1844	-0.002	0.5503	0.0615	0.1904	109.5581	116.6156	55.2677
31	0.4682	-0.1709	-0.6155	0.1418	0.2178	1.1262	-0.1349	-0.129	-0.0903	-0.0837	0.1887	0.0397	0.4693	0.1306	-0.0265	0.7279	-0.1955	-0.1882	0.6074	0.0568	0.1692	107.5863	126.6229	46.2252
32	6.881	1.6595	2.4865	0.6968	0.0834	2.7439	0.0851	0.0092	-0.0085	-0.2653	-0.1463	0.2363	0.2389	-0.5388	0.0686	1.2092	-0.204	-0.3347	0.4213	-0.0555	0.5709	98.7142	120.1256	48.6534

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A
2	X-RAY DIFFRACTION	2	chain B
3	X-RAY DIFFRACTION	3	chain C
4	X-RAY DIFFRACTION	4	chain D
5	X-RAY DIFFRACTION	5	chain E
6	X-RAY DIFFRACTION	6	chain F
7	X-RAY DIFFRACTION	7	chain G
8	X-RAY DIFFRACTION	8	chain H
9	X-RAY DIFFRACTION	9	chain I
10	X-RAY DIFFRACTION	10	chain J
11	X-RAY DIFFRACTION	11	chain K
12	X-RAY DIFFRACTION	12	chain L
13	X-RAY DIFFRACTION	13	chain M
14	X-RAY DIFFRACTION	14	chain N
15	X-RAY DIFFRACTION	15	chain O
16	X-RAY DIFFRACTION	16	chain P
17	X-RAY DIFFRACTION	17	chain Q
18	X-RAY DIFFRACTION	18	chain R
19	X-RAY DIFFRACTION	19	chain S
20	X-RAY DIFFRACTION	20	chain T
21	X-RAY DIFFRACTION	21	chain U
22	X-RAY DIFFRACTION	22	chain V
23	X-RAY DIFFRACTION	23	chain W
24	X-RAY DIFFRACTION	24	chain X
25	X-RAY DIFFRACTION	25	chain Y
26	X-RAY DIFFRACTION	26	chain Z
27	X-RAY DIFFRACTION	27	chain a
28	X-RAY DIFFRACTION	28	chain b
29	X-RAY DIFFRACTION	29	chain c
30	X-RAY DIFFRACTION	30	chain d
31	X-RAY DIFFRACTION	31	chain e
32	X-RAY DIFFRACTION	32	chain f

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