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- PDB-5tdp: Crystal structure of the Fab fragment of anti-HER2 antibody 4D5 w... -

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Basic information

Entry
Database: PDB / ID: 5tdp
TitleCrystal structure of the Fab fragment of anti-HER2 antibody 4D5 with redesigned heavy and light chain interfaces
Components
  • anti-HER2 Fab Heavy Chain
  • anti-HER2 Fab Light Chain
KeywordsIMMUNE SYSTEM / antibody / immunoglobulin / Fab / 4D5
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.716 Å
AuthorsYin, Y. / Carter, P.J.
CitationJournal: To Be Published
Title: Crystal structure of the Fab fragment of anti-HER2 antibody 4D5 with redesigned heavy and light chain interfaces
Authors: Yin, Y. / Carter, P.J.
History
DepositionSep 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: anti-HER2 Fab Light Chain
B: anti-HER2 Fab Heavy Chain
C: anti-HER2 Fab Light Chain
D: anti-HER2 Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,3175
Polymers94,2254
Non-polymers921
Water8,629479
1
A: anti-HER2 Fab Light Chain
B: anti-HER2 Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2053
Polymers47,1132
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-26 kcal/mol
Surface area19190 Å2
MethodPISA
2
C: anti-HER2 Fab Light Chain
D: anti-HER2 Fab Heavy Chain


Theoretical massNumber of molelcules
Total (without water)47,1132
Polymers47,1132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-28 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.038, 79.746, 85.738
Angle α, β, γ (deg.)113.780, 93.070, 102.410
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody anti-HER2 Fab Light Chain


Mass: 23385.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#2: Antibody anti-HER2 Fab Heavy Chain


Mass: 23727.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3,350, 0.04 M Citrate, 0.06 M BTP, pH6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.716→43.705 Å / Num. obs: 92819 / % possible obs: 95.5 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.084 / Net I/av σ(I): 20.618 / Net I/σ(I): 9.2
Reflection shellResolution: 1.72→1.78 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.487 / CC1/2: 0.757 / % possible all: 94.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å43.71 Å
Translation3.5 Å43.71 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.9_1692refinement
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FVE

1fve


Resolution: 1.716→43.705 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.82
RfactorNum. reflection% reflection
Rfree0.2516 4731 5.1 %
Rwork0.2202 --
obs0.2218 92809 95.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.54 Å2 / Biso mean: 27.8452 Å2 / Biso min: 6.69 Å2
Refinement stepCycle: final / Resolution: 1.716→43.705 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6445 0 6 479 6930
Biso mean--45 28.73 -
Num. residues----848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076736
X-RAY DIFFRACTIONf_angle_d1.0959174
X-RAY DIFFRACTIONf_chiral_restr0.0431035
X-RAY DIFFRACTIONf_plane_restr0.0051183
X-RAY DIFFRACTIONf_dihedral_angle_d13.292412
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7157-1.73520.30761210.27872410253179
1.7352-1.75560.31961770.26052926310395
1.7556-1.7770.26321550.26043012316795
1.777-1.79950.26271550.24632857301295
1.7995-1.82320.29621350.25272933306895
1.8232-1.84810.28411690.24532976314595
1.8481-1.87450.31191520.2482890304295
1.8745-1.90250.28731450.23312900304594
1.9025-1.93220.28571740.22992936311095
1.9322-1.96390.25971490.22772935308494
1.9639-1.99780.28131500.23432888303895
1.9978-2.03410.26361680.22692917308594
2.0341-2.07320.24231640.22442911307594
2.0732-2.11560.26311790.2262875305495
2.1156-2.16160.28851390.22433016315595
2.1616-2.21180.25621680.22332850301895
2.2118-2.26720.24561410.21972991313295
2.2672-2.32840.27651570.22682941309896
2.3284-2.3970.27821370.23362993313096
2.397-2.47430.31421580.23792954311296
2.4743-2.56270.29481580.23963012317097
2.5627-2.66530.28931790.24063017319697
2.6653-2.78660.29751520.24273000315297
2.7866-2.93350.25611380.24342992313097
2.9335-3.11730.28541680.22922984315297
3.1173-3.35790.24641720.22542971314396
3.3579-3.69560.22321770.21072917309495
3.6956-4.230.20151410.19312961310295
4.23-5.32790.19141740.16953075324999
5.3279-43.71960.20611790.20063038321799
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
11.4006-0.097-0.10543.54063.07775.45490.0688-0.13310.07940.5167-0.31440.27290.0909-0.246-0.07430.5029-0.11330.03710.3091-0.09420.19945.209557.780639.0106
21.94131.0025-1.71423.1951-1.67734.41710.2319-0.2716-0.0780.3447-0.3335-0.135-0.320.3437-0.03990.1844-0.0514-0.02290.25370.03630.154534.682124.461552.1528
31.9045-0.3906-0.0232.7473-0.31581.1956-0.0395-0.0584-0.02180.1454-0.02430.083-0.15360.0484-0.00130.0847-0.0034-0.00840.1016-0.00340.094147.79546.768619.1931
40.93730.2241-0.69861.508-0.6761.25840.0062-0.07130.01440.07170.04810.1302-0.1609-0.48270.030.10530.09390.0180.42210.02310.130428.133326.045437.1218
51.7881-0.5447-0.32082.25511.39265.7362-0.1080.0238-0.04760.0022-0.02180.05860.52810.0767-0.01120.30880.0207-0.03060.2019-0.0140.148931.201427.0258-17.4703
60.8806-0.68310.14324.3408-0.06332.17490.1301-0.021-0.1375-0.34640.03590.24130.24-0.02250.02830.15450.01-0.01060.14390.01790.239141.6505-2.23433.1428
71.63940.2921-0.50992.1584-0.58091.9505-0.04350.00190.0167-0.2157-0.00490.0419-0.03780.05310.00190.0805-0.009-0.02430.09040.00380.094929.135738.00881.7927
81.0668-1.2532-0.51482.06520.57640.8581-0.0550.0103-0.1931-0.05160.0775-0.0514-0.02840.06190.00680.1023-0.00370.02650.1532-0.03380.259748.586211.41289.3811
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resseq 2:108))A2 - 108
2X-RAY DIFFRACTION2chain 'A' and ((resseq 109:214))A109 - 214
3X-RAY DIFFRACTION3chain 'B' and ((resseq 1:120))B1 - 120
4X-RAY DIFFRACTION4chain 'B' and ((resseq 121:220))B121 - 220
5X-RAY DIFFRACTION5chain 'C' and ((resseq 2:108))C2 - 108
6X-RAY DIFFRACTION6chain 'C' and ((resseq 109:214))C109 - 214
7X-RAY DIFFRACTION7chain 'D' and ((resseq 1:120))D1 - 120
8X-RAY DIFFRACTION8chain 'D' and ((resseq 121:220))D121 - 220

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