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- PDB-6b9z: Trastuzumab Fab v3 -

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Basic information

Entry
Database: PDB / ID: 6b9z
TitleTrastuzumab Fab v3
Components
  • Immunoglobulin G binding protein A
  • Protein L
  • Trastuzumab Fab heavy chain
  • Trastuzumab Fab light chain
KeywordsIMMUNE SYSTEM / monoclonal antibody / Fab
Function / homology
Function and homology information


IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / cell envelope / IgG binding / Classical antibody-mediated complement activation ...IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / cell envelope / IgG binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin binding / immunoglobulin mediated immune response / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / blood microparticle / adaptive immune response / Potential therapeutics for SARS / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Protein G-related albumin-binding (GA) module / Extracellular matrix-binding protein ebh, GA module / GA module / GA module / Protein L, Ig light chain-binding / Protein L b1 domain / Repeat of unknown function DUF5633 / Family of unknown function (DUF5633) / Immunoglobulin FC, subunit C / Octapeptide repeat ...Protein G-related albumin-binding (GA) module / Extracellular matrix-binding protein ebh, GA module / GA module / GA module / Protein L, Ig light chain-binding / Protein L b1 domain / Repeat of unknown function DUF5633 / Family of unknown function (DUF5633) / Immunoglobulin FC, subunit C / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Ubiquitin-like (UB roll) - #10 / GA-like domain / GA-like domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / : / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ubiquitin-like (UB roll) / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Roll / Immunoglobulin-like fold / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Immunoglobulin kappa constant / Immunoglobulin G-binding protein A / Immunoglobulin G binding protein A / Protein L / IgG H chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
Finegoldia magna (bacteria)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsBzymek, K.P. / King, J.D. / Williams, J.C.
CitationJournal: Bioconjug. Chem. / Year: 2018
Title: Template-Catalyzed, Disulfide Conjugation of Monoclonal Antibodies Using a Natural Amino Acid Tag.
Authors: King, J.D. / Ma, Y. / Kuo, Y.C. / Bzymek, K.P. / Goodstein, L.H. / Meyer, K. / Moore, R.E. / Crow, D. / Colcher, D.M. / Singh, G. / Horne, D.A. / Williams, J.C.
History
DepositionOct 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: 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
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trastuzumab Fab light chain
B: Trastuzumab Fab heavy chain
E: Protein L
C: Immunoglobulin G binding protein A


Theoretical massNumber of molelcules
Total (without water)60,2864
Polymers60,2864
Non-polymers00
Water10,323573
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-30 kcal/mol
Surface area24470 Å2
Unit cell
Length a, b, c (Å)53.490, 105.290, 117.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Trastuzumab Fab light chain / HERCEPTIN Fab light chain


Mass: 23518.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: IGKC / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P01834
#2: Antibody Trastuzumab Fab heavy chain / HERCEPTIN Fab heavy chain


Mass: 23822.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CSO is partially oxidized cysteine
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: S6B291
#3: Protein Protein L


Mass: 6907.657 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Finegoldia magna (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q51918
#4: Antibody Immunoglobulin G binding protein A


Mass: 6037.530 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: spa / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2UW42, UniProt: P02976*PLUS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 573 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.74 Å3/Da / Density % sol: 55.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris, pH 7.5, 24 mM NaCl, 15% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.82→39.5 Å / Num. obs: 59094 / % possible obs: 98.3 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Net I/σ(I): 16.8
Reflection shellResolution: 1.82→1.87 Å / Redundancy: 14 % / Rmerge(I) obs: 0.76 / CC1/2: 0.657 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IOI

4ioi


Resolution: 1.82→39.5 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.39
RfactorNum. reflection% reflection
Rfree0.189 2952 5 %
Rwork0.165 --
obs0.166 59086 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.82→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4224 0 0 573 4797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064463
X-RAY DIFFRACTIONf_angle_d0.846108
X-RAY DIFFRACTIONf_dihedral_angle_d12.9212737
X-RAY DIFFRACTIONf_chiral_restr0.056687
X-RAY DIFFRACTIONf_plane_restr0.005795
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.84990.30771380.26172634X-RAY DIFFRACTION98
1.8499-1.88180.28571380.22922619X-RAY DIFFRACTION98
1.8818-1.9160.27721390.21712635X-RAY DIFFRACTION98
1.916-1.95290.24221390.21252635X-RAY DIFFRACTION98
1.9529-1.99270.25721380.19662629X-RAY DIFFRACTION98
1.9927-2.0360.21831380.18862647X-RAY DIFFRACTION98
2.036-2.08340.22961390.1952642X-RAY DIFFRACTION98
2.0834-2.13550.21691400.1822662X-RAY DIFFRACTION98
2.1355-2.19320.27181330.17862537X-RAY DIFFRACTION94
2.1932-2.25780.19771400.17832658X-RAY DIFFRACTION99
2.2578-2.33060.19651400.16862666X-RAY DIFFRACTION99
2.3306-2.41390.20261410.17582680X-RAY DIFFRACTION99
2.4139-2.51060.21331410.17292668X-RAY DIFFRACTION99
2.5106-2.62480.19841420.17122697X-RAY DIFFRACTION99
2.6248-2.76310.18391410.17462687X-RAY DIFFRACTION99
2.7631-2.93620.191370.17372603X-RAY DIFFRACTION95
2.9362-3.16280.2171440.16592730X-RAY DIFFRACTION100
3.1628-3.48090.17371440.15672729X-RAY DIFFRACTION100
3.4809-3.98420.1621440.14422742X-RAY DIFFRACTION100
3.9842-5.01810.12131440.12252729X-RAY DIFFRACTION97
5.0181-39.5080.18141520.16242905X-RAY DIFFRACTION99
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)
16.1767-1.3872-2.98954.5224-0.56614.13930.14430.23210.4866-0.0475-0.0237-0.1155-0.33230.0277-0.04550.2236-0.0352-0.00360.22480.010.280626.111543.71578.6261
24.7717-4.704-0.94174.70870.65945.82040.1636-0.83620.470.31670.48770.1293-0.47650.4624-0.68510.4529-0.05920.0350.3868-0.01160.508228.451548.908912.5991
38.8599-1.79925.25295.3596-1.72545.52650.51681.0489-0.3274-0.725-0.27540.83510.1006-0.6986-0.19060.54580.114-0.01080.5908-0.05060.413524.7195-14.0023-1.7538
45.3216-4.18831.88663.8215-1.50232.96140.09670.0447-0.1774-0.2769-0.06180.04930.19030.0615-0.04080.24970.0122-0.00220.173-0.01850.208928.0741-8.45767.7912
56.3453-3.35625.14945.4112-2.82364.22560.23930.42810.3404-0.6411-0.4011-0.76470.15820.35640.07540.31340.06310.10260.29630.01660.285733.0077-3.51462.0223
61.0447-0.1118-0.22371.80380.97292.13630.00210.01510.0547-0.00150.0247-0.0078-0.0597-0.0906-0.0330.1610.0108-0.00580.21080.01240.208314.100129.5189.5017
72.36811.88863.07911.7512.56813.9690.0547-0.0577-0.0343-0.0993-0.0679-0.0118-0.15970.0306-0.07230.21280.0249-0.01490.19040.00640.194520.457137.78127.4492
84.0407-3.35651.99667.1784-1.91352.43570.14680.046-0.22490.37650.1586-0.13940.45730.3381-0.22670.38210.0617-0.08590.2701-0.07910.186531.642525.976142.8677
94.6646-0.11225.14362.4454-0.33715.7697-0.01290.00540.16120.03270.0998-0.63170.12690.9548-0.09470.30330.0463-0.03030.5361-0.12650.409439.723427.246838.825
101.7103-1.24031.1792.5679-0.12.61670.0848-0.1151-0.10410.46830.1973-0.45470.34110.331-0.1660.33120.0487-0.08290.2735-0.03740.267132.676329.046543.4668
111.72250.09530.06341.7785-0.07633.0794-0.3675-0.43210.05660.36250.3015-0.04430.13450.01970.09090.25410.0056-0.0140.16690.01140.212419.6814.241718.303
128.3548-4.18161.75453.6809-2.03672.85070.0488-0.0028-0.58760.02490.15240.30840.2398-0.2103-0.22470.1987-0.05080.00880.1989-0.00470.29467.99214.111410.8885
132.9649-0.76070.48725.37430.94522.44630.03660.13750.0722-0.2442-0.04-0.1722-0.00130.091-0.00920.17820.01840.00990.19340.04260.167719.05619.75415.4019
141.8571-1.10060.28533.7531-0.31931.4231-0.06520.05450.07970.07090.09470.08950.0331-0.0706-0.02940.1573-0.01080.00260.19240.00410.166615.0958.17610.6131
150.1145-0.0405-0.34091.92422.15483.0186-0.0033-0.08790.01820.71790.1293-0.08770.64890.2718-0.16440.40060.0607-0.06890.2728-0.03210.23827.460914.457238.2519
164.1863-4.4472-2.36086.55085.19425.11070.24410.1672-0.28660.2546-0.17750.06760.41560.0013-0.07780.46220.0027-0.01940.20930.00430.228522.743514.655338.4491
172.367-2.0212-1.49444.48322.74753.83370.130.00830.04120.3416-0.02760.06660.4910.0334-0.07380.3746-0.025-0.01360.2098-0.0240.194421.305617.437140.0673
184.6106-1.9537-2.13813.55275.69119.6677-0.0905-0.3646-0.4751.3039-0.26270.09241.0498-0.22290.23470.91340.00050.03010.23780.03790.345721.174410.408846.9523
195.9589-5.6589-1.0215.62260.89856.0292-0.2281-0.4138-0.42880.39630.28620.3433-0.33230.1616-0.00060.2572-0.0480.02670.2534-0.03760.473226.141644.261115.1712
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'E' AND (RESID 34 THROUGH 69 )
2X-RAY DIFFRACTION2CHAIN 'E' AND (RESID 70 THROUGH 81 )
3X-RAY DIFFRACTION3CHAIN 'C' AND (RESID 1 THROUGH 16 )
4X-RAY DIFFRACTION4CHAIN 'C' AND (RESID 17 THROUGH 35 )
5X-RAY DIFFRACTION5CHAIN 'C' AND (RESID 36 THROUGH 54 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 1 THROUGH 101 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 102 THROUGH 113 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 114 THROUGH 150 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 151 THROUGH 163 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 164 THROUGH 214 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 1 THROUGH 17 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 18 THROUGH 32 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 33 THROUGH 67 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 68 THROUGH 113 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 114 THROUGH 141 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 142 THROUGH 164 )
17X-RAY DIFFRACTION17CHAIN 'B' AND (RESID 165 THROUGH 210 )
18X-RAY DIFFRACTION18CHAIN 'B' AND (RESID 211 THROUGH 221 )
19X-RAY DIFFRACTION19CHAIN 'E' AND (RESID 19 THROUGH 33 )

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