PDB-8zmw: Structure of a triple-helix region of human Collagen type VII fro...

ID or keywords:

Entry

Database: PDB / ID: 8zmw

Title

Structure of a triple-helix region of human Collagen type VII from Trautec

Components

collagen type VII

Keywords

STRUCTURAL PROTEIN / Human collagen VII / Triple-helix

Function / homology

ACETATE ION

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Chu, Y. / Zhai, Y. / Fan, X. / Fu, S. / Li, J. / Wu, X. / Cai, H. / Wang, X. / Li, D. / Feng, P. ...

Funding support

1items

Citation

Journal: To Be Published
Title: Structure of a triple-helix region of human Collagen type VII from Trautec
Authors: Chu, Y. / Zhai, Y. / Fan, X. / Fu, S. / Li, J. / Wu, X. / Cai, H. / Wang, X. / Li, D. / Feng, P. / Cao, K. / Qian, S.

History

Deposition	May 24, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 26, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8zmw.cif.gz	50.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8zmw.ent.gz	38.1 KB	Display	PDB format
PDBx/mmJSON format	8zmw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zm/8zmw ftp://data.pdbj.org/pub/pdb/validation_reports/zm/8zmw	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: collagen type VII

B: collagen type VII

C: collagen type VII

D: collagen type VII

E: collagen type VII

F: collagen type VII

hetero molecules

17.2 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: collagen type VII

B: collagen type VII

C: collagen type VII

hetero molecules

defined by author&software
Evidence: homology
8.63 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: collagen type VII

E: collagen type VII

F: collagen type VII

defined by author&software
8.57 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	20.927, 30.425, 53.078
Angle α, β, γ (deg.)	78.396, 81.644, 72.831
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 1 - 30 / Label seq-ID: 1 - 30

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30

#1: Protein/peptide	collagen type VII Mass: 2857.037 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 1.84 Å³/Da / Density % sol: 33.05 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Crystal-B6 (0.2M MgAc2, 0.1M Sodium cacodylate pH6.5, 20% PEG 8000)

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 15, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97853 Å / Relative weight: 1
Reflection	Resolution: 1.75→28.66 Å / Num. obs: 11871 / % possible obs: 96.6 % / Redundancy: 3.4 % / CC_1/2: 0.999 / Net I/σ(I): 15.3
Reflection shell	Resolution: 1.75→1.78 Å / Num. unique obs: 607 / CC_1/2: 0.99

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.75→28.659 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.935 / SU B: 2.022 / SU ML: 0.066 / Cross valid method: FREE R-VALUE / ESU R: 0.131 / ESU R Free: 0.128
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1928	555	4.676 %
R_work	0.1331	11315	-
all	0.136	-	-
obs	-	11870	96.614 %

Solvent computation

Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 13.123 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.103 Å²	-0.7 Å²	-0.644 Å²
2-	-	0.225 Å²	0.262 Å²
3-	-	-	-0.776 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→28.659 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1210	0	4	316	1530

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.012	1304
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.014	1082
X-RAY DIFFRACTION	r_angle_refined_deg	1.798	1.792	1840
X-RAY DIFFRACTION	r_angle_other_deg	1.204	1.574	2654
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.859	5	176
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	17.509	15.306	49
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.187	15	74
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.357	15	18
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	157
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	1487
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	181
X-RAY DIFFRACTION	r_nbd_refined	0.197	0.2	434
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.192	0.2	999
X-RAY DIFFRACTION	r_nbtor_refined	0.167	0.2	715
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.09	0.2	447
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.181	0.2	181
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.119	0.2	15
X-RAY DIFFRACTION	r_nbd_other	0.194	0.2	75
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.163	0.2	77
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.194	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	0.956	1.16	717
X-RAY DIFFRACTION	r_mcbond_other	0.955	1.159	714
X-RAY DIFFRACTION	r_mcangle_it	1.611	1.713	885
X-RAY DIFFRACTION	r_mcangle_other	1.611	1.713	885
X-RAY DIFFRACTION	r_scbond_it	1.063	1.327	587
X-RAY DIFFRACTION	r_scbond_other	1.062	1.326	588
X-RAY DIFFRACTION	r_scangle_it	1.695	1.946	954
X-RAY DIFFRACTION	r_scangle_other	1.694	1.946	955
X-RAY DIFFRACTION	r_lrange_it	4.195	17.522	1613
X-RAY DIFFRACTION	r_lrange_other	3.896	16.646	1526
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.122	0.05	530
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.128	0.05	526
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.123	0.05	524
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.104	0.05	530
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.131	0.05	526
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.119	0.05	541
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.13	0.05	535
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.107	0.05	535
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.135	0.05	542
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.104	0.05	528
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.103	0.05	524
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.119	0.05	526
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.122	0.05	522
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.116	0.05	528
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.122	0.05	524

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.1223	0.05005
1	2	B	X-RAY DIFFRACTION	Local ncs	0.1223	0.05005
2	3	A	X-RAY DIFFRACTION	Local ncs	0.12844	0.05005
2	4	C	X-RAY DIFFRACTION	Local ncs	0.12844	0.05005
3	5	A	X-RAY DIFFRACTION	Local ncs	0.12301	0.05005
3	6	D	X-RAY DIFFRACTION	Local ncs	0.12301	0.05005
4	7	A	X-RAY DIFFRACTION	Local ncs	0.10376	0.05006
4	8	E	X-RAY DIFFRACTION	Local ncs	0.10376	0.05006
5	9	A	X-RAY DIFFRACTION	Local ncs	0.13106	0.05005
5	10	F	X-RAY DIFFRACTION	Local ncs	0.13106	0.05005
6	11	B	X-RAY DIFFRACTION	Local ncs	0.11918	0.05005
6	12	C	X-RAY DIFFRACTION	Local ncs	0.11918	0.05005
7	13	B	X-RAY DIFFRACTION	Local ncs	0.12974	0.05005
7	14	D	X-RAY DIFFRACTION	Local ncs	0.12974	0.05005
8	15	B	X-RAY DIFFRACTION	Local ncs	0.10708	0.05005
8	16	E	X-RAY DIFFRACTION	Local ncs	0.10708	0.05005
9	17	B	X-RAY DIFFRACTION	Local ncs	0.13537	0.05006
9	18	F	X-RAY DIFFRACTION	Local ncs	0.13537	0.05006
10	19	C	X-RAY DIFFRACTION	Local ncs	0.10416	0.05005
10	20	D	X-RAY DIFFRACTION	Local ncs	0.10416	0.05005
11	21	C	X-RAY DIFFRACTION	Local ncs	0.10323	0.05005
11	22	E	X-RAY DIFFRACTION	Local ncs	0.10323	0.05005
12	23	C	X-RAY DIFFRACTION	Local ncs	0.11852	0.05005
12	24	F	X-RAY DIFFRACTION	Local ncs	0.11852	0.05005
13	25	D	X-RAY DIFFRACTION	Local ncs	0.12159	0.05005
13	26	E	X-RAY DIFFRACTION	Local ncs	0.12159	0.05005
14	27	D	X-RAY DIFFRACTION	Local ncs	0.11588	0.05006
14	28	F	X-RAY DIFFRACTION	Local ncs	0.11588	0.05006
15	29	E	X-RAY DIFFRACTION	Local ncs	0.12237	0.05005
15	30	F	X-RAY DIFFRACTION	Local ncs	0.12237	0.05005

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.75-1.795	0.213	44	0.159	789	0.162	878	0.937	0.955	94.8747	0.155
1.795-1.844	0.233	44	0.146	810	0.15	897	0.929	0.96	95.2062	0.141
1.844-1.898	0.237	46	0.136	804	0.141	893	0.95	0.964	95.1848	0.136
1.898-1.956	0.189	42	0.139	729	0.142	801	0.951	0.964	96.2547	0.14
1.956-2.02	0.167	25	0.136	746	0.137	805	0.961	0.967	95.7764	0.145
2.02-2.09	0.188	38	0.125	732	0.129	801	0.964	0.97	96.1298	0.133
2.09-2.169	0.172	35	0.126	679	0.129	740	0.961	0.971	96.4865	0.136
2.169-2.257	0.202	42	0.134	668	0.137	735	0.945	0.968	96.5986	0.146
2.257-2.356	0.165	43	0.113	634	0.117	700	0.969	0.973	96.7143	0.126
2.356-2.47	0.226	27	0.124	604	0.127	652	0.932	0.971	96.7791	0.138
2.47-2.603	0.153	31	0.12	620	0.122	664	0.965	0.971	98.0422	0.137
2.603-2.759	0.172	19	0.119	548	0.12	582	0.957	0.974	97.4227	0.138
2.759-2.948	0.144	19	0.112	530	0.114	567	0.977	0.979	96.8254	0.134
2.948-3.181	0.138	21	0.124	484	0.125	514	0.97	0.974	98.249	0.147
3.181-3.481	0.239	14	0.122	484	0.124	510	0.947	0.976	97.6471	0.149
3.481-3.884	0.126	11	0.123	402	0.123	419	0.968	0.98	98.568	0.154
3.884-4.472	0.161	11	0.111	372	0.112	390	0.964	0.981	98.2051	0.14
4.472-5.444	0.156	10	0.168	320	0.168	333	0.96	0.972	99.0991	0.216
5.444-7.563	0.437	18	0.23	233	0.241	255	0.888	0.958	98.4314	0.289
7.563-28.659	0.295	15	0.35	126	0.344	148	0.899	0.933	95.2703	0.466

-
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