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- PDB-9n8q: Crystal structure of Trastuzumab Fab with P151A -

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Basic information

Entry
Database: PDB / ID: 9n8q
TitleCrystal structure of Trastuzumab Fab with P151A
Components
  • Trastuzumab Fab Heavy chain
  • Trastuzumab Fab Light chain
KeywordsIMMUNE SYSTEM / HUMAN FAB FRAGMENT / IMMUNE RESPONSE / ProAla / Proline-to-alanine / bispecific antibody / bsAb / bsIgG / Cis-peptide / Trastuzumab / Fab
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChoi, W.S. / Tilegenova, C. / Are, M. / Zwolak, A. / Shaffer, P. / Sharma, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Folding-Mediated Secretion of Pure Bispecific Antibodies
Authors: Tilegenova, C. / Liu, T. / Zhao, Q. / Are, M. / Zhao, Y. / Choi, W.S. / Bhaumik, A. / Steele, R. / Manieri, N. / Turegun, B. / Shaffer, P. / Ernst, R. / Sharma, S. / Cheung, W. / Zwolak, A.
History
DepositionFeb 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Trastuzumab Fab Heavy chain
L: Trastuzumab Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4646
Polymers48,0392
Non-polymers4244
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-19 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.191, 99.191, 211.338
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11L-301-

PEG

21L-301-

PEG

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Components

#1: Antibody Trastuzumab Fab Heavy chain


Mass: 24605.527 Da / Num. of mol.: 1 / Mutation: P151A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Trastuzumab Fab Light chain


Mass: 23433.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.12 Å3/Da / Density % sol: 60.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.019M Disodium ATP, 0.1M Sodium Cacodylate pH 6.5, 18.6% w/v PEG 10,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976254 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 13, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 2.12→85.89 Å / Num. obs: 35686 / % possible obs: 100 % / Redundancy: 39.8 % / Biso Wilson estimate: 58.45 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.037 / Net I/σ(I): 12.8
Reflection shellResolution: 2.12→2.16 Å / Redundancy: 40.4 % / Mean I/σ(I) obs: 0.2 / Num. unique obs: 1756 / CC1/2: 0.34 / Rpim(I) all: 6.24 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→45 Å / SU ML: 0.4128 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.4825
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2776 964 4.93 %
Rwork0.2131 18585 -
obs0.2163 19549 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.02 Å2
Refinement stepCycle: LAST / Resolution: 2.6→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3216 0 28 74 3318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083329
X-RAY DIFFRACTIONf_angle_d0.95744531
X-RAY DIFFRACTIONf_chiral_restr0.053512
X-RAY DIFFRACTIONf_plane_restr0.0084582
X-RAY DIFFRACTIONf_dihedral_angle_d9.1545477
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.740.40421370.31712556X-RAY DIFFRACTION99.45
2.74-2.910.35391250.27382613X-RAY DIFFRACTION99.71
2.91-3.140.39011410.29132578X-RAY DIFFRACTION99.96
3.14-3.450.32721320.23872640X-RAY DIFFRACTION99.82
3.45-3.950.28021280.22122655X-RAY DIFFRACTION99.96
3.95-4.980.22061410.16442686X-RAY DIFFRACTION99.89
4.98-450.24681600.19372857X-RAY DIFFRACTION99.77
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)
10.6891444621610.09432884209110.07965555633420.3102113115760.3667786396530.590254311311-0.1744704711770.1413873413510.1227766613650.0163056212808-0.00331413266679-0.0605111927143-0.04379074530210.291862895438-1.37785392115E-50.647603157529-0.0172988165362-0.09601868451440.3496581977330.03317096040310.55347757951111.8585032912-23.7430118998-16.8693656343
20.0503313261976-0.03446093451360.003687393436620.040499201630.01979911558490.0356816140530.1916983262170.0698433345418-0.3769461421090.43981895255-0.0593633989134-0.1254675014330.3079331234780.0711999427389-0.0003926316780.793861316130.0908685700188-0.1009574469860.5303697594480.06778972294650.6325927101958.19754781389-34.686329996-24.050795383
32.085635471160.765674298579-0.6024377434680.232014936022-0.2438134100220.166339674591-0.247567255657-0.9609821271460.3239535136990.284006090894-0.128426018088-0.1163208512410.8164111605080.241479810967-0.2297580667471.18633462033-0.2060947547230.03674598642930.4242808181480.03603278787590.459513695224-6.94551916285-32.69543119445.98505777501
41.35282052041-0.05554452714370.2649553963550.2451432495680.1733645638560.397580828833-0.2568297166470.2848838472360.1439202576220.01986102608390.166617253290.04545955445130.560304468491-0.232870377460.0002820836260610.650909001698-0.1691641341450.01011606375730.3608496361190.008969036848030.504684527798-6.62167299562-33.2765305776-29.0558614402
50.130712159198-0.09279392434760.195171707770.150764004469-0.1846063467760.201646517692-0.07140643157960.231781428956-0.04408590428670.362179717205-0.105565783241-0.128229918638-0.157119724467-0.0380336940741-0.0001000486730290.576552309503-0.1625795596220.01080123572140.2941280630630.03242871996790.560924515299-10.2169052102-30.0454286271-22.6818721518
60.526615090134-0.2032769087510.1909991868480.201882087628-0.0122824875720.235636906771-0.113629858022-0.9334914823430.2483753067840.1913775957080.01398772594080.3969627426140.241198084904-0.6804727919810.02869155383421.0386299788-0.4040602422250.1865786068510.851958282831-0.2601421097990.649632608101-21.93826114-27.03277935175.51140205379
70.2981096258580.602630449577-0.05740543642561.435998805360.3672732726660.984369349120.192548172003-0.887989786353-0.4069825307180.406346845869-0.7356395527230.1761859425770.379319631652-0.0985467890449-0.5508772633860.672426816164-0.4256757864330.1371963429710.866495105056-0.2665174846430.396562856003-24.3661142148-29.19680940115.16225455464
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'H' and (resid 1 through 94 )HA1 - 941 - 98
22chain 'H' and (resid 95 through 106 )HA95 - 10699 - 113
33chain 'H' and (resid 107 through 217 )HA107 - 217114 - 215
44chain 'L' and (resid 1 through 90 )LF1 - 901 - 90
55chain 'L' and (resid 91 through 113 )LF91 - 11391 - 113
66chain 'L' and (resid 114 through 163 )LF114 - 163114 - 163
77chain 'L' and (resid 164 through 213 )LF164 - 213164 - 213

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