4ONG

Fab fragment of 3D6 in complex with amyloid beta 1-40

PDB DOI: https://doi.org/10.2210/pdb4ONG/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, Homo sapiens
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2014-01-28 Released: 2014-06-11
Deposition Author(s): Feinberg, H., Saldanha, J.W., Diep, L., Goel, A., Widom, A., Veldman, G.M., Weis, W.I., Schenk, D., Basi, G.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.227
R-Value Work: 0.177
R-Value Observed: 0.180

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure reveals conservation of amyloid-beta conformation recognized by 3D6 following humanization to bapineuzumab.

Feinberg, H., Saldanha, J.W., Diep, L., Goel, A., Widom, A., Veldman, G.M., Weis, W.I., Schenk, D., Basi, G.S.

(2014) Alzheimers Res Ther 6: 31-31

PubMed: 25024748 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1186/alzrt261
Primary Citation of Related Structures:
4ONF, 4ONG

PubMed Abstract:
Immunotherapy targeting amyloid-β peptide is under active clinical investigation for treatment of Alzheimer's disease (AD). Among the hypotheses being investigated for impact on clinical outcome are the preferred epitope or conformation of amyloid-β to target for treatment, and the mechanism of action underlying immunotherapy. Bapineuzumab (humanized 3D6), a neo-epitope specific antibody recognizing amyloid-β1-5 with strong preference for an exposed Asp residue at the N-terminus of the peptide, has undergone advanced clinical testing for treatment of AD.

Organizational Affiliation

Departments of Structural Biology and of Molecular & Cellular Physiology, 299 Campus Drive, Stanford University School of Medicine, Stanford, CA 94305, USA.

Macromolecule Content

Total Structure Weight: 54.79 kDa
Atom Count: 3,626
Modelled Residue Count: 429
Deposited Residue Count: 481
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3D6 FAB ANTIBODY HEAVY CHAIN	A [auth H]	222	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
3D6 FAB ANTIBODY LIGHT CHAIN	B [auth L]	219	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Amyloid beta A4 protein	C [auth P]	40	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P05067 (Homo sapiens) Explore P05067 Go to UniProtKB: P05067
PHAROS: P05067 GTEx: ENSG00000142192
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05067
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain LA [auth L] SDF format, chain Q [auth H] SDF format, chain R [auth H] MOL2 format, chain LA [auth L] MOL2 format, chain Q [auth H] MOL2 format, chain R [auth H]	LA [auth L], Q [auth H], R [auth H]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain LA [auth L] Focus chain Q [auth H] Focus chain R [auth H] Interactions & Density Focus chain LA [auth L] Focus chain Q [auth H] Focus chain R [auth H]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth H] SDF format, chain GA [auth L] SDF format, chain H SDF format, chain HA [auth L] SDF format, chain KA [auth L] SDF format, chain M [auth H] SDF format, chain O [auth H] SDF format, chain AA [auth L] SDF format, chain BA [auth L] SDF format, chain CA [auth L] SDF format, chain D [auth H] SDF format, chain DA [auth L] SDF format, chain EA [auth L] SDF format, chain F [auth H] SDF format, chain FA [auth L] SDF format, chain G [auth H] SDF format, chain I [auth H] SDF format, chain IA [auth L] SDF format, chain J [auth H] SDF format, chain JA [auth L] SDF format, chain K [auth H] SDF format, chain L [auth H] SDF format, chain N [auth H] SDF format, chain P [auth H] SDF format, chain X [auth L] SDF format, chain Y [auth L] SDF format, chain Z [auth L] MOL2 format, chain E [auth H] MOL2 format, chain GA [auth L] MOL2 format, chain H MOL2 format, chain HA [auth L] MOL2 format, chain KA [auth L] MOL2 format, chain M [auth H] MOL2 format, chain O [auth H] MOL2 format, chain AA [auth L] MOL2 format, chain BA [auth L] MOL2 format, chain CA [auth L] MOL2 format, chain D [auth H] MOL2 format, chain DA [auth L] MOL2 format, chain EA [auth L] MOL2 format, chain F [auth H] MOL2 format, chain FA [auth L] MOL2 format, chain G [auth H] MOL2 format, chain I [auth H] MOL2 format, chain IA [auth L] MOL2 format, chain J [auth H] MOL2 format, chain JA [auth L] MOL2 format, chain K [auth H] MOL2 format, chain L [auth H] MOL2 format, chain N [auth H] MOL2 format, chain P [auth H] MOL2 format, chain X [auth L] MOL2 format, chain Y [auth L] MOL2 format, chain Z [auth L]	AA [auth L] BA [auth L] CA [auth L] D [auth H] DA [auth L] AA [auth L], BA [auth L], CA [auth L], D [auth H], DA [auth L], E [auth H], EA [auth L], F [auth H], FA [auth L], G [auth H], GA [auth L], H, HA [auth L], I [auth H], IA [auth L], J [auth H], JA [auth L], K [auth H], KA [auth L], L [auth H], M [auth H], N [auth H], O [auth H], P [auth H], X [auth L], Y [auth L], Z [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth L] Focus chain BA [auth L] Focus chain CA [auth L] Focus chain D [auth H] Focus chain DA [auth L] Focus chain E [auth H] Focus chain EA [auth L] Focus chain F [auth H] Focus chain FA [auth L] Focus chain G [auth H] Focus chain GA [auth L] Focus chain H Focus chain HA [auth L] Focus chain I [auth H] Focus chain IA [auth L] Focus chain J [auth H] Focus chain JA [auth L] Focus chain K [auth H] Focus chain KA [auth L] Focus chain L [auth H] Focus chain M [auth H] Focus chain N [auth H] Focus chain O [auth H] Focus chain P [auth H] Focus chain X [auth L] Focus chain Y [auth L] Focus chain Z [auth L] Interactions & Density Focus chain AA [auth L] Focus chain BA [auth L] Focus chain CA [auth L] Focus chain D [auth H] Focus chain DA [auth L] Focus chain E [auth H] Focus chain EA [auth L] Focus chain F [auth H] Focus chain FA [auth L] Focus chain G [auth H] Focus chain GA [auth L] Focus chain H Focus chain HA [auth L] Focus chain I [auth H] Focus chain IA [auth L] Focus chain J [auth H] Focus chain JA [auth L] Focus chain K [auth H] Focus chain KA [auth L] Focus chain L [auth H] Focus chain M [auth H] Focus chain N [auth H] Focus chain O [auth H] Focus chain P [auth H] Focus chain X [auth L] Focus chain Y [auth L] Focus chain Z [auth L]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain MA [auth L] SDF format, chain NA [auth L] SDF format, chain T [auth H] SDF format, chain V [auth H] SDF format, chain W [auth H] SDF format, chain OA [auth L] SDF format, chain PA [auth L] SDF format, chain QA [auth L] SDF format, chain RA [auth L] SDF format, chain S [auth H] SDF format, chain U [auth H] MOL2 format, chain MA [auth L] MOL2 format, chain NA [auth L] MOL2 format, chain T [auth H] MOL2 format, chain V [auth H] MOL2 format, chain W [auth H] MOL2 format, chain OA [auth L] MOL2 format, chain PA [auth L] MOL2 format, chain QA [auth L] MOL2 format, chain RA [auth L] MOL2 format, chain S [auth H] MOL2 format, chain U [auth H]	MA [auth L] NA [auth L] OA [auth L] PA [auth L] QA [auth L] MA [auth L], NA [auth L], OA [auth L], PA [auth L], QA [auth L], RA [auth L], S [auth H], T [auth H], U [auth H], V [auth H], W [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain MA [auth L] Focus chain NA [auth L] Focus chain OA [auth L] Focus chain PA [auth L] Focus chain QA [auth L] Focus chain RA [auth L] Focus chain S [auth H] Focus chain T [auth H] Focus chain U [auth H] Focus chain V [auth H] Focus chain W [auth H] Interactions & Density Focus chain MA [auth L] Focus chain NA [auth L] Focus chain OA [auth L] Focus chain PA [auth L] Focus chain QA [auth L] Focus chain RA [auth L] Focus chain S [auth H] Focus chain T [auth H] Focus chain U [auth H] Focus chain V [auth H] Focus chain W [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.227
R-Value Work: 0.177
R-Value Observed: 0.180
Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.04	α = 90
b = 84.94	β = 90
c = 175.69	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
COMO	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-06-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-06-11
Type: Initial release
Version 1.1: 2014-07-30
Changes: Database references
Version 1.2: 2017-11-22
Changes: Refinement description
Version 1.3: 2024-04-03
Changes: Data collection, Database references, Derived calculations, Refinement description