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- PDB-6mh2: Structure of Herceptin Fab without antigen -

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Basic information

Entry
Database: PDB / ID: 6mh2
TitleStructure of Herceptin Fab without antigen
Components
  • Herceptin Fab arm heavy chain
  • Herceptin Fab arm light chain
KeywordsIMMUNE SYSTEM / Herceptin / antibody / Fab fragment
Function / homology
Function and homology information


immune response / extracellular space
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig-like domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsLuthra, A. / Langley, D.B. / Christie, M. / Christ, D.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1113904 Australia
Australian Research Council (ARC)160104915 Australia
CitationJournal: Biochemistry / Year: 2019
Title: Human Antibody Bispecifics through Phage Display Selection.
Authors: Luthra, A. / Langley, D.B. / Schofield, P. / Jackson, J. / Abdelatti, M. / Rouet, R. / Nevoltris, D. / Mazigi, O. / Crossett, B. / Christie, M. / Christ, D.
History
DepositionSep 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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: Herceptin Fab arm light chain
B: Herceptin Fab arm heavy chain
C: Herceptin Fab arm light chain
D: Herceptin Fab arm heavy chain


Theoretical massNumber of molelcules
Total (without water)96,3674
Polymers96,3674
Non-polymers00
Water00
1
A: Herceptin Fab arm light chain
B: Herceptin Fab arm heavy chain


Theoretical massNumber of molelcules
Total (without water)48,1842
Polymers48,1842
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-23 kcal/mol
Surface area18340 Å2
MethodPISA
2
C: Herceptin Fab arm light chain
D: Herceptin Fab arm heavy chain


Theoretical massNumber of molelcules
Total (without water)48,1842
Polymers48,1842
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-22 kcal/mol
Surface area18190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.990, 78.890, 85.140
Angle α, β, γ (deg.)113.590, 92.780, 101.680
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody Herceptin Fab arm light chain


Mass: 23466.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 HEK / Production host: Homo sapiens (human) / References: UniProt: Q7Z3Y4
#2: Antibody Herceptin Fab arm heavy chain


Mass: 24717.592 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 HEK / Production host: Homo sapiens (human)

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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: 2.42 Å3/Da / Density % sol: 49.1 % / Description: plate-like
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 200 mM ammonium acetate, 100 mM Bis-Tris, pH 5.5, 25% v/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.8→43.61 Å / Num. obs: 19572 / % possible obs: 90.5 % / Redundancy: 3.4 % / CC1/2: 0.977 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.073 / Rrim(I) all: 0.137 / Net I/σ(I): 7.3 / Num. measured all: 66134 / Scaling rejects: 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.8-2.953.40.3851008729520.8620.240.4552.592.5
8.85-43.613.50.06122156400.9930.0380.07213.793.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.85 Å42.08 Å
Translation5.85 Å42.08 Å

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
MOSFLMdata reduction
Aimless0.5.26data scaling
PHASER2.6.1phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1N8Z

1n8z


Resolution: 2.8→42.08 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.837 / WRfactor Rfree: 0.3148 / WRfactor Rwork: 0.256 / FOM work R set: 0.6962 / SU B: 54.515 / SU ML: 0.468 / SU R Cruickshank DPI: 0.424 / SU Rfree: 0.5005 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.501 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3062 956 4.9 %RANDOM
Rwork0.2511 ---
obs0.2538 18615 90.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 137.15 Å2 / Biso mean: 53.676 Å2 / Biso min: 25.74 Å2
Baniso -1Baniso -2Baniso -3
1--3.25 Å20.81 Å2-2.43 Å2
2--5.35 Å23.58 Å2
3----4 Å2
Refinement stepCycle: final / Resolution: 2.8→42.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5738 0 0 0 5738
Num. residues----821
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135891
X-RAY DIFFRACTIONr_bond_other_d0.0080.0174847
X-RAY DIFFRACTIONr_angle_refined_deg1.6251.6428114
X-RAY DIFFRACTIONr_angle_other_deg1.4881.56411116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6235810
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.56622.727209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.17715649
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.71514
X-RAY DIFFRACTIONr_chiral_restr0.0640.2839
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026901
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021249
LS refinement shellResolution: 2.8→2.872 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 76 -
Rwork0.361 1419 -
all-1495 -
obs--92.46 %
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)
10.4821-0.20920.50333.3877-0.28310.570.04120.09-0.1756-0.21190.0628-0.19790.00260.0165-0.1040.4848-0.03270.15780.1758-0.21390.308311.1198106.1687-25.059
21.0352-0.21750.69661.9470.66480.81780.0417-0.1113-0.1346-0.1120.122-0.1912-0.0295-0.0511-0.16380.4513-0.08420.16210.1928-0.22220.340412.4723119.1324-11.8208
30.98710.81270.17182.9932-2.08963.02950.2475-0.8740.05960.1423-0.4798-0.2408-0.4454-0.25850.23230.5586-0.36270.22790.8502-0.170.205616.7834137.846327.4989
40.72720.7368-0.18760.8495-0.4062.1670.0439-0.21740.0092-0.0475-0.0602-0.1298-0.0603-0.23640.01640.3998-0.12240.15570.2977-0.22930.281216.2494131.76739.2245
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 214
2X-RAY DIFFRACTION2B1 - 220
3X-RAY DIFFRACTION3C1 - 214
4X-RAY DIFFRACTION4D1 - 220

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