PDB-7e6p: Fab-amyloid beta fragment complex

ID or keywords:

Entry

Database: PDB / ID: 7e6p

Title

Fab-amyloid beta fragment complex

Components

Amyloid beta fragment with an intramolecular disulfide bond at positions 17 and 28
Fab Heavy chain
Fab Light chain

Keywords

IMMUNE SYSTEM / Fab complex

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DI(HYDROXYETHYL)ETHER

Function and homology information

Biological species

Mus musculus (house mouse)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Kita, A. / Irie, K. / Irie, Y. / Miki, K.

Funding support

Japan, 1items

Citation

Journal: Acs Chem Neurosci / Year: 2021
Title: Characterization of a Conformation-Restricted Amyloid beta Peptide and Immunoreactivity of Its Antibody in Human AD brain.
Authors: Kageyama, Y. / Irie, Y. / Matsushima, Y. / Segawa, T. / Bellier, J.P. / Hidaka, K. / Sugiyama, H. / Kaneda, D. / Hashizume, Y. / Akatsu, H. / Miki, K. / Kita, A. / Walker, D.G. / Irie, K. / Tooyama, I.

History

Deposition	Feb 23, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 5, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 23, 2024	Group: Data collection / Derived calculations / Structure summary Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7e6p.cif.gz	104.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7e6p.ent.gz	76.4 KB	Display	PDB format
PDBx/mmJSON format	7e6p.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7e6p_validation.pdf.gz	464.4 KB	Display	wwPDB validaton report
Full document	7e6p_full_validation.pdf.gz	467.8 KB	Display
Data in XML	7e6p_validation.xml.gz	21.2 KB	Display
Data in CIF	7e6p_validation.cif.gz	27.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e6/7e6p ftp://data.pdbj.org/pub/pdb/validation_reports/e6/7e6p	HTTPS FTP

-
Related structure data

Similar structure data	2a6d-2 6pbw-d 6vbo-d 5kzp-2 6umj-d 2dqt-d 3mlt-2 5u15-2 3mlu-d 7c94-1 6vbp-4 5tpp-d 2qhr-d 7c94-2 6vbq-2 1kel-d 5muq-2 6b5t-d 6gk8-d 6vrt-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

L: Fab Heavy chain

H: Fab Light chain

A: Amyloid beta fragment with an intramolecular disulfide bond at positions 17 and 28

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	185.049, 40.464, 69.379
Angle α, β, γ (deg.)	90.000, 97.219, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	H-417- HOH

-
Protein/peptide , 1 types, 1 molecules A

#3: Protein/peptide	Amyloid beta fragment with an intramolecular disulfide bond at positions 17 and 28 Mass: 1675.860 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Antibody , 2 types, 2 molecules LH

#1: Antibody	Fab Heavy chain Mass: 24356.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody	Fab Light chain Mass: 23750.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

-
Non-polymers , 3 types, 96 molecules

#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	N
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.59 Å³/Da / Density % sol: 52.47 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / Details: PEGMME5000, magnesium formate, sodium acetate

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Dec 12, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.5→45.9 Å / Num. obs: 18065 / % possible obs: 100 % / Redundancy: 6.8 % / CC_1/2: 0.998 / Net I/σ(I): 17
Reflection shell	Resolution: 2.5→2.6 Å / Num. unique obs: 2008 / CC_1/2: 0.958

-
Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.5→45.9 Å / Cor.coef. F_o:F_c: 0.938 / Cor.coef. F_o:F_c free: 0.9 / SU B: 8.916 / SU ML: 0.199 / Cross valid method: FREE R-VALUE / ESU R: 0.531 / ESU R Free: 0.282

	R_factor	Num. reflection	% reflection
R_free	0.244	873	4.833 %
R_work	0.1913	17192	-
all	0.194	-	-
obs	-	18065	99.917 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 29.257 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.496 Å²	-0 Å²	1.09 Å²
2-	-	-1.358 Å²	0 Å²
3-	-	-	1.528 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→45.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3436	0	25	91	3552

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.003	0.013	3548
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	3212
X-RAY DIFFRACTION	r_angle_refined_deg	1.277	1.646	4829
X-RAY DIFFRACTION	r_angle_other_deg	1.246	1.574	7444
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.802	5	445
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.709	23.506	154
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.457	15	548
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.447	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.055	0.2	469
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	4013
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	791
X-RAY DIFFRACTION	r_nbd_refined	0.186	0.2	536
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.211	0.2	2831
X-RAY DIFFRACTION	r_nbtor_refined	0.161	0.2	1640
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	1594
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.127	0.2	122
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.043	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.358	0.2	10
X-RAY DIFFRACTION	r_nbd_other	0.213	0.2	57
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.144	0.2	10
X-RAY DIFFRACTION	r_mcbond_it	2.235	2.986	1792
X-RAY DIFFRACTION	r_mcbond_other	2.235	2.985	1791
X-RAY DIFFRACTION	r_mcangle_it	3.601	4.463	2233
X-RAY DIFFRACTION	r_mcangle_other	3.6	4.464	2234
X-RAY DIFFRACTION	r_scbond_it	2.533	3.209	1756
X-RAY DIFFRACTION	r_scbond_other	2.569	3.208	1757
X-RAY DIFFRACTION	r_scangle_it	4.008	4.679	2596
X-RAY DIFFRACTION	r_scangle_other	4.025	4.678	2597
X-RAY DIFFRACTION	r_lrange_it	5.773	33.492	3637
X-RAY DIFFRACTION	r_lrange_other	5.802	33.485	3638

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 (%)
2.5-2.565	0.339	45	0.266	1283	X-RAY DIFFRACTION	100
2.565-2.635	0.346	66	0.244	1222	X-RAY DIFFRACTION	100
2.635-2.712	0.418	73	0.23	1178	X-RAY DIFFRACTION	99.9201
2.712-2.795	0.244	46	0.214	1154	X-RAY DIFFRACTION	100
2.795-2.886	0.257	64	0.195	1145	X-RAY DIFFRACTION	100
2.886-2.988	0.221	48	0.183	1073	X-RAY DIFFRACTION	99.7331
2.988-3.1	0.203	61	0.184	1048	X-RAY DIFFRACTION	100
3.1-3.227	0.215	60	0.186	993	X-RAY DIFFRACTION	99.8104
3.227-3.37	0.2	45	0.199	986	X-RAY DIFFRACTION	99.9031
3.37-3.534	0.252	42	0.195	915	X-RAY DIFFRACTION	100
3.534-3.725	0.223	48	0.203	885	X-RAY DIFFRACTION	100
3.725-3.951	0.263	49	0.176	848	X-RAY DIFFRACTION	100
3.951-4.223	0.224	39	0.16	788	X-RAY DIFFRACTION	100
4.223-4.561	0.179	53	0.147	729	X-RAY DIFFRACTION	100
4.561-4.995	0.24	24	0.168	707	X-RAY DIFFRACTION	99.8634
4.995-5.582	0.243	32	0.186	611	X-RAY DIFFRACTION	100
5.582-6.442	0.234	29	0.189	551	X-RAY DIFFRACTION	99.8279
6.442-7.88	0.295	21	0.192	477	X-RAY DIFFRACTION	100
7.88-11.103	0.179	16	0.15	377	X-RAY DIFFRACTION	100
11.103-45.9	0.407	12	0.342	222	X-RAY DIFFRACTION	97.5

-
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

-
Protein/peptide , 1 types, 1 molecules A

-
Antibody , 2 types, 2 molecules LH

-
Non-polymers , 3 types, 96 molecules

-
Details

-
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

-Protein/peptide , 1 types, 1 molecules A

-Antibody , 2 types, 2 molecules LH

-Non-polymers , 3 types, 96 molecules

-Details

-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

-
Protein/peptide , 1 types, 1 molecules A

-
Antibody , 2 types, 2 molecules LH

-
Non-polymers , 3 types, 96 molecules

-
Details

-
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