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- PDB-1i9r: STRUCTURE OF CD40L IN COMPLEX WITH THE FAB FRAGMENT OF HUMANIZED ... -

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Basic information

Entry
Database: PDB / ID: 1i9r
TitleSTRUCTURE OF CD40L IN COMPLEX WITH THE FAB FRAGMENT OF HUMANIZED 5C8 ANTIBODY
Components
  • CD40 LIGAND
  • IMMUNOGLOBULIN H
  • IMMUNOGLOBULIN L
KeywordsCYTOKINE/IMMUNE SYSTEM / beta-sheet sandwich / immunoglobulin / CYTOKINE-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


CD40 receptor binding / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / CD40 signaling pathway / isotype switching / tumor necrosis factor receptor binding / regulation of immunoglobulin production / positive regulation of extrinsic apoptotic signaling pathway / leukocyte cell-cell adhesion / positive regulation of interleukin-4 production / B cell proliferation ...CD40 receptor binding / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / CD40 signaling pathway / isotype switching / tumor necrosis factor receptor binding / regulation of immunoglobulin production / positive regulation of extrinsic apoptotic signaling pathway / leukocyte cell-cell adhesion / positive regulation of interleukin-4 production / B cell proliferation / positive regulation of interleukin-10 production / positive regulation of endothelial cell apoptotic process / T cell costimulation / positive regulation of T cell proliferation / positive regulation of interleukin-12 production / B cell differentiation / protein serine/threonine kinase activator activity / cytokine activity / integrin-mediated signaling pathway / TNFR2 non-canonical NF-kB pathway / positive regulation of NF-kappaB transcription factor activity / platelet activation / integrin binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell surface receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / inflammatory response / external side of plasma membrane / negative regulation of apoptotic process / cell surface / Golgi apparatus / extracellular space / membrane / plasma membrane
Similarity search - Function
CD40 ligand / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNF(Tumour Necrosis Factor) family / Jelly Rolls - #40 / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumour necrosis factor-like domain superfamily / Jelly Rolls ...CD40 ligand / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNF(Tumour Necrosis Factor) family / Jelly Rolls - #40 / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumour necrosis factor-like domain superfamily / Jelly Rolls / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsKarpusas, M. / Lucci, J. / Ferrant, J. / Benjamin, C. / Hsu, Y.-M.
CitationJournal: Structure / Year: 2001
Title: Structure of CD40 ligand in complex with the Fab fragment of a neutralizing humanized antibody.
Authors: Karpusas, M. / Lucci, J. / Ferrant, J. / Benjamin, C. / Taylor, F.R. / Strauch, K. / Garber, E. / Hsu, Y.M.
History
DepositionMar 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 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: CD40 LIGAND
B: CD40 LIGAND
C: CD40 LIGAND
H: IMMUNOGLOBULIN H
L: IMMUNOGLOBULIN L
K: IMMUNOGLOBULIN H
M: IMMUNOGLOBULIN L
X: IMMUNOGLOBULIN H
Y: IMMUNOGLOBULIN L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,19112
Polymers188,9959
Non-polymers1963
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)224.48, 129.91, 96.49
Angle α, β, γ (deg.)90.0, 109.6, 90.0
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CD40 LIGAND / CD40-L


Mass: 15812.817 Da / Num. of mol.: 3 / Fragment: RESIDUES 116-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Pichia pastoris (fungus) / References: UniProt: P29965
#2: Antibody IMMUNOGLOBULIN H


Mass: 23304.039 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: NSO MYELOMA
#3: Antibody IMMUNOGLOBULIN L


Mass: 23881.500 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: NSO MYELOMA
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
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: 3.1 Å3/Da / Density % sol: 60.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG MME 550, 0.1 M MES, 0.01 M zinc sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-15 mg/mlprotein1drop
220 %(w/v)PEG550 MME1reservoir
30.1 MMES1reservoirpH6.5
40.01 Mzinc sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 11, 1999 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.1→35 Å / Num. all: 71662 / Num. obs: 46508 / % possible obs: 96.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 7.52
Reflection shellResolution: 3.1→3.21 Å / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 1.97 / % possible all: 87.7
Reflection
*PLUS
Lowest resolution: 35 Å
Reflection shell
*PLUS
% possible obs: 87.7 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR98refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1aly

1aly


Resolution: 3.1→35 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
Details: For NCS the following 3 chain groups were used: a) A, H, L, b) B,K, X c) C, M, Y. The final rms deviation of main chain atoms between groups is 0.18 Angstrom.
RfactorNum. reflectionSelection details
Rfree0.285 2325 RANDOM
Rwork0.233 --
all0.233 46508 -
obs0.233 71662 -
Refinement stepCycle: LAST / Resolution: 3.1→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13167 0 3 0 13170
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_deg1.89
Refinement
*PLUS
Lowest resolution: 35 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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