PDB-6c4y: Cross-alpha Amyloid-like Structure alphaAmG

ID or keywords:

Entry

Database: PDB / ID: 6c4y

Title

Cross-alpha Amyloid-like Structure alphaAmG

Components

Cross-alpha Amyloid-like Structure alphaAmG

Keywords

DE NOVO PROTEIN / Protein Design / Cross-alpha Amyloid

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.5 Å

Authors

Liu, L. / Zhang, S.Q.

Funding support

United States, 1items

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	Jan 13, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 15, 2018	Provider: repository / Type: Initial release
Revision 1.1	Aug 29, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6c4y.cif.gz	191.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6c4y.ent.gz	166.9 KB	Display	PDB format
PDBx/mmJSON format	6c4y.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6c4y_validation.pdf.gz	448.3 KB	Display	wwPDB validaton report
Full document	6c4y_full_validation.pdf.gz	448.1 KB	Display
Data in XML	6c4y_validation.xml.gz	15.8 KB	Display
Data in CIF	6c4y_validation.cif.gz	22.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c4/6c4y ftp://data.pdbj.org/pub/pdb/validation_reports/c4/6c4y	HTTPS FTP

-
Related structure data

Related structure data	6c4xC 6c4zC 6c50C 6c51C 6c52C 6d02C 6o3nC C: citing same article (ref.)
Similar structure data	6c4z-d 1zxe-1 5dzs-2 3o5u-d 3zu6-d 5d4v-2 7ddz-d 4ewh-d 5y3n-d 3o6r-d Search similar-shape structures by Omokage search (details)

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: Cross-alpha Amyloid-like Structure alphaAmG

B: Cross-alpha Amyloid-like Structure alphaAmG

C: Cross-alpha Amyloid-like Structure alphaAmG

D: Cross-alpha Amyloid-like Structure alphaAmG

E: Cross-alpha Amyloid-like Structure alphaAmG

F: Cross-alpha Amyloid-like Structure alphaAmG

G: Cross-alpha Amyloid-like Structure alphaAmG

H: Cross-alpha Amyloid-like Structure alphaAmG

K: Cross-alpha Amyloid-like Structure alphaAmG

I: Cross-alpha Amyloid-like Structure alphaAmG

J: Cross-alpha Amyloid-like Structure alphaAmG

L: Cross-alpha Amyloid-like Structure alphaAmG

M: Cross-alpha Amyloid-like Structure alphaAmG

N: Cross-alpha Amyloid-like Structure alphaAmG

O: Cross-alpha Amyloid-like Structure alphaAmG

P: Cross-alpha Amyloid-like Structure alphaAmG

Q: Cross-alpha Amyloid-like Structure alphaAmG

R: Cross-alpha Amyloid-like Structure alphaAmG

52.5 kDa, 18 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: Fibrils formed detected by Cryo-EM

Unit cell

Length a, b, c (Å)	125.241, 125.241, 119.026
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	95
Space group name H-M	P4₃22

Components on special symmetry positions

ID	Model	Components
1	1	R-102- HOH

#1: Protein/peptide	Cross-alpha Amyloid-like Structure alphaAmG Mass: 2918.543 Da / Num. of mol.: 18 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 4.44 Å³/Da / Density % sol: 72.31 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.2 M ammonium acetate, 0.1 M tri-sodium citrate pH 5.6, 30% (w/v) MPD

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / 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: 2.49→126 Å / Num. obs: 62540 / % possible obs: 100 % / Redundancy: 8.8 % / Net I/σ(I): 19.2
Reflection shell	Resolution: 2.49→2.58 Å

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
MOLREP		phasing

Refinement

Resolution: 2.5→125.24 Å / Cor.coef. F_o:F_c: 0.938 / Cor.coef. F_o:F_c free: 0.932 / SU B: 21.953 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.287 / ESU R Free: 0.227 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25916	1716	5.2 %	RANDOM
R_work	0.23677	-	-	-
obs	0.23799	31602	99.7 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 70.838 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.64 Å²	-0 Å²	-0 Å²
2-	-	1.64 Å²	-0 Å²
3-	-	-	-3.29 Å²

Refinement step

Cycle: 1 / Resolution: 2.5→125.24 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3696	0	0	18	3714

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.019	3769
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	4069
X-RAY DIFFRACTION	r_angle_refined_deg	0.915	2.058	5024
X-RAY DIFFRACTION	r_angle_other_deg	0.804	3	9398
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.417	5	440
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.664	21.517	145
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.142	15	852
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.075	15	21
X-RAY DIFFRACTION	r_chiral_restr	0.04	0.2	580
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	3854
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	683
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	0.515	3.927	1847
X-RAY DIFFRACTION	r_mcbond_other	0.514	3.927	1845
X-RAY DIFFRACTION	r_mcangle_it	0.892	5.882	2285
X-RAY DIFFRACTION	r_mcangle_other	0.892	5.882	2284
X-RAY DIFFRACTION	r_scbond_it	0.404	3.996	1922
X-RAY DIFFRACTION	r_scbond_other	0.404	3.996	1923
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	0.747	5.977	2737
X-RAY DIFFRACTION	r_long_range_B_refined	2.383	71.74	13580
X-RAY DIFFRACTION	r_long_range_B_other	2.384	71.738	13577
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.499→2.564 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.366	95	-
R_work	0.357	2228	-
obs	-	-	96.39 %

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	18.8665	-1.9878	16.8632	7.9887	-5.1109	21.5292	-0.6695	0.0309	0.8489	0.0692	-0.0135	-0.2838	-0.56	0.2062	0.6831	0.2278	-0.0075	0.1665	0.1985	-0.0329	0.2426	4.945	36.238	56.851
2	7.343	0.5696	5.7013	0.646	2.9467	16.0852	0.3513	-0.1503	-0.8085	0.3298	0.0765	0.0598	1.9922	-0.2008	-0.4277	0.6321	-0.1157	0.1905	0.2472	0.1366	0.4758	2.972	26.625	55.941
3	13.1513	-6.6782	11.841	10.7081	-5.4444	14.7775	-0.6828	-0.4188	0.5771	0.588	0.0823	-0.4581	-0.735	0.3334	0.6006	0.2437	-0.0083	0.1567	0.2749	0.0029	0.2263	14.223	34.392	54.4
4	2.784	-2.466	4.7751	9.9681	-9.3681	16.2525	0.0884	-0.1528	-0.6113	-0.3998	0.3957	0.1272	1.3366	-0.1393	-0.4842	0.3369	0.0302	0.1818	0.1658	0.0226	0.3035	11.473	25.58	50.995
5	11.2067	-10.4103	8.9324	28.913	-12.7172	8.2192	-0.7973	-0.5365	-0.0103	0.7658	0.592	-0.9525	-0.5819	-0.2631	0.2053	0.3436	0.1556	0.1903	0.4366	-0.0312	0.2054	23.496	32.597	48.645
6	1.7907	-2.1001	4.4267	14.4661	-11.7792	16.2508	0.0895	-0.1146	-0.3836	-1.1053	0.5864	1.0475	1.3656	-0.2594	-0.6758	0.3187	0.0091	0.1759	0.1557	0.0755	0.3779	18.048	26.609	43.075
7	2.5116	-4.6518	3.3535	23.8903	-3.5982	5.222	-0.3142	-0.2244	0.1136	1.2638	0.1132	-0.6052	-0.1509	-0.0445	0.201	0.2983	0.113	0.1997	0.3649	0.0519	0.257	31.613	28.224	44.719
8	3.2421	1.8377	1.1899	26.1916	-13.6175	10.3461	0.0735	0.0884	-0.3105	-1.1193	0.5386	0.892	0.9397	-0.17	-0.6122	0.3475	-0.002	0.1963	0.1338	-0.0176	0.3159	25.861	24.741	37.564
9	4.5198	5.9609	3.0471	24.5798	4.8885	6.9197	-0.0777	-0.4743	-0.2166	0.8704	0.1254	-0.6072	0.4168	0.2838	-0.0478	0.2328	0.0523	0.1603	0.2696	-0.0311	0.2169	45.266	19.334	31.091
10	4.8206	1.1331	1.6675	30.9477	-0.419	2.2237	0.0041	-0.2302	-0.0296	0.9913	-0.096	-1.3957	0.1343	0.3972	0.092	0.2473	0.0321	0.1592	0.2806	-0.0085	0.2637	39.801	24.832	37.793
11	6.1625	4.7184	0.3279	14.8885	-5.5004	5.5842	-0.5361	0.0087	0.3955	-1.3951	0.4895	1.0234	0.39	-0.5542	0.0466	0.3478	-0.0102	0.0862	0.1006	-0.0056	0.3143	32.593	25.244	31.09
12	10.2601	10.6222	0.6714	21.2474	-2.3439	2.9518	-0.3766	0.1894	0.4499	-1.0564	0.2995	0.9491	0.1989	-0.1239	0.0772	0.2351	-0.0102	0.136	0.1808	-0.0307	0.255	39.209	22.614	24.28
13	11.307	9.0352	7.7279	22.0212	8.7175	8.3534	0.1484	-0.2641	-0.1906	0.8912	-0.0036	-0.2856	0.6123	0.5143	-0.1449	0.2155	0.0664	0.1243	0.2381	-0.0304	0.1526	52.176	17.513	23.088
14	11.7011	8.8537	1.3154	13.9911	-0.6257	2.2608	-0.9654	-0.0145	0.9237	-0.6768	0.4898	0.9026	-0.3596	-0.1503	0.4756	0.2488	-0.0443	0.0022	0.1637	-0.0689	0.3128	46.47	23.654	18.1
15	15.0147	9.2293	12.7393	11.1586	5.0827	14.0055	0.4086	-0.4162	-0.5804	0.6355	-0.2338	-0.2629	0.6981	0.0093	-0.1748	0.2286	0.0401	0.144	0.2246	-0.0064	0.167	55.443	13.843	14.085
16	12.2444	4.4831	6.6009	9.2025	0.1976	6.1144	-0.8194	-0.0283	1.6317	-0.6032	-0.0609	0.9253	-0.3599	0.1303	0.8803	0.1466	-0.1011	-0.0436	0.1467	-0.1032	0.3152	52.465	22.396	10.078
17	19.8733	2.7884	19.9639	8.8865	4.6466	21.219	0.7739	-0.5041	-0.8377	0.0094	-0.3095	-0.1074	1.1336	-0.3442	-0.4643	0.2399	0.0378	0.172	0.2016	0.0806	0.2365	61.308	12.982	4.656
18	19.7121	3.4297	5.6849	3.0147	0.4767	1.7503	-0.7046	-0.0776	1.5339	0.2308	0.2148	0.0961	-0.2673	-0.0693	0.4898	0.1408	0.0057	-0.0158	0.1727	-0.0482	0.1959	60.024	22.742	4.382

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 26
2	X-RAY DIFFRACTION	2	B	0 - 26
3	X-RAY DIFFRACTION	3	C	0 - 26
4	X-RAY DIFFRACTION	4	D	0 - 26
5	X-RAY DIFFRACTION	5	E	0 - 26
6	X-RAY DIFFRACTION	6	F	0 - 26
7	X-RAY DIFFRACTION	7	G	0 - 26
8	X-RAY DIFFRACTION	8	H	0 - 26
9	X-RAY DIFFRACTION	9	K	0 - 26
10	X-RAY DIFFRACTION	10	I	0 - 26
11	X-RAY DIFFRACTION	11	J	0 - 26
12	X-RAY DIFFRACTION	12	L	0 - 26
13	X-RAY DIFFRACTION	13	M	0 - 26
14	X-RAY DIFFRACTION	14	N	0 - 26
15	X-RAY DIFFRACTION	15	O	0 - 26
16	X-RAY DIFFRACTION	16	P	0 - 26
17	X-RAY DIFFRACTION	17	Q	0 - 26
18	X-RAY DIFFRACTION	18	R	0 - 26

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and 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

-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

-
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