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- PDB-8che: TLT-1 binding Fab of the bispecific antibody HMB-001 in complex w... -

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Basic information

Entry
Database: PDB / ID: 8che
TitleTLT-1 binding Fab of the bispecific antibody HMB-001 in complex with the TLT-1 stalk peptide
Components
  • Fab heavy chain
  • Fab light chain
  • Trem-like transcript 1 protein
KeywordsBLOOD CLOTTING / TLT-1 / Fab / Bispecific Antibody / HMB-001
Function / homology
Function and homology information


platelet alpha granule / calcium-mediated signaling / platelet activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transmembrane signaling receptor activity / nuclear speck / innate immune response / cell surface / Golgi apparatus / signal transduction ...platelet alpha granule / calcium-mediated signaling / platelet activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transmembrane signaling receptor activity / nuclear speck / innate immune response / cell surface / Golgi apparatus / signal transduction / membrane / plasma membrane / cytosol
Similarity search - Function
: / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Trem-like transcript 1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsJohansson, E. / Schluckebier, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Cardiovasc Res / Year: 2024
Title: A bispecific antibody approach for the potential prophylactic treatment of inherited bleeding disorders.
Authors: Gandhi, P.S. / Zivkovic, M. / Ostergaard, H. / Bonde, A.C. / Elm, T. / Lovgreen, M.N. / Schluckebier, G. / Johansson, E. / Olsen, O.H. / Olsen, E.H.N. / de Bus, I.A. / Bloem, K. / Alskar, O. ...Authors: Gandhi, P.S. / Zivkovic, M. / Ostergaard, H. / Bonde, A.C. / Elm, T. / Lovgreen, M.N. / Schluckebier, G. / Johansson, E. / Olsen, O.H. / Olsen, E.H.N. / de Bus, I.A. / Bloem, K. / Alskar, O. / Rea, C.J. / Bjorn, S.E. / Schutgens, R.E. / Sorensen, B. / Urbanus, R.T. / Faber, J.H.
History
DepositionFeb 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Sep 11, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 20, 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
H: Fab heavy chain
L: Fab light chain
A: Fab heavy chain
B: Fab light chain
C: Trem-like transcript 1 protein
D: Trem-like transcript 1 protein


Theoretical massNumber of molelcules
Total (without water)102,0366
Polymers102,0366
Non-polymers00
Water18,3211017
1
H: Fab heavy chain
L: Fab light chain
C: Trem-like transcript 1 protein


Theoretical massNumber of molelcules
Total (without water)51,0183
Polymers51,0183
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-41 kcal/mol
Surface area19850 Å2
MethodPISA
2
A: Fab heavy chain
B: Fab light chain
D: Trem-like transcript 1 protein


Theoretical massNumber of molelcules
Total (without water)51,0183
Polymers51,0183
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-40 kcal/mol
Surface area19750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.234, 65.377, 67.145
Angle α, β, γ (deg.)91.880, 91.720, 92.890
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Antibody Fab heavy chain


Mass: 22847.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Fab light chain


Mass: 24213.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide Trem-like transcript 1 protein / TLT-1 / Triggering receptor expressed on myeloid cells-like protein 1


Mass: 3957.113 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q86YW5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1017 / 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: 2.28 Å3/Da / Density % sol: 46.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 1M lithium chloride, 20% (w/v) PEG 6000, 100 mM citric acid/NaOH, pH 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.49→28.46 Å / Num. obs: 140068 / % possible obs: 91.03 % / Redundancy: 1.9 % / Biso Wilson estimate: 18.72 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.05225 / Rpim(I) all: 0.05222 / Rrim(I) all: 0.07387 / Net I/σ(I): 9.03
Reflection shellResolution: 1.49→1.543 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.5929 / Mean I/σ(I) obs: 1.37 / Num. unique obs: 25651 / CC1/2: 0.0678 / CC star: 0.356 / Rpim(I) all: 0.5928 / Rrim(I) all: 0.8384 / % possible all: 62.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→28.46 Å / SU ML: 0.1661 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 19.0085
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.174 1783 1.33 %
Rwork0.157 132575 -
obs0.1572 134358 91.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.02 Å2
Refinement stepCycle: LAST / Resolution: 1.49→28.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6814 0 0 1019 7833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00877204
X-RAY DIFFRACTIONf_angle_d0.95489850
X-RAY DIFFRACTIONf_chiral_restr0.08141114
X-RAY DIFFRACTIONf_plane_restr0.00811283
X-RAY DIFFRACTIONf_dihedral_angle_d6.15061023
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.530.3144890.30736773X-RAY DIFFRACTION60.54
1.53-1.580.28561200.24438293X-RAY DIFFRACTION74.18
1.58-1.630.19581390.203810412X-RAY DIFFRACTION93.04
1.63-1.680.23391390.183710521X-RAY DIFFRACTION93.85
1.68-1.750.17681570.172510492X-RAY DIFFRACTION93.81
1.75-1.830.22771370.166610544X-RAY DIFFRACTION93.96
1.83-1.930.18231510.167210626X-RAY DIFFRACTION94.88
1.93-2.050.17611320.150110713X-RAY DIFFRACTION95.44
2.05-2.210.15751460.145210715X-RAY DIFFRACTION95.83
2.21-2.430.19121380.1510819X-RAY DIFFRACTION96.19
2.43-2.780.18671420.152510758X-RAY DIFFRACTION96.23
2.78-3.50.16561500.150610938X-RAY DIFFRACTION97.71
3.5-28.460.14121430.147110971X-RAY DIFFRACTION97.86
Refinement TLS params.Method: refined / Origin x: -2.35225873292 Å / Origin y: -12.2897337815 Å / Origin z: -32.8803688976 Å
111213212223313233
T0.152205416008 Å2-0.00453644742021 Å2-0.000724188355809 Å2-0.153335052736 Å20.00155378730192 Å2--0.144384449733 Å2
L0.152153645672 °2-0.0409103721056 °2-0.0124195155119 °2-0.208220003814 °20.0576974788263 °2--0.155494665376 °2
S0.0220194161803 Å °0.000771765239171 Å °0.0141790864102 Å °-0.00377899678831 Å °-0.00846743719577 Å °-0.0282186290621 Å °-0.0181236046915 Å °0.0145098863851 Å °-0.015463784782 Å °
Refinement TLS groupSelection details: all

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