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- PDB-1h0d: Crystal structure of Human Angiogenin in complex with Fab fragmen... -

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Basic information

Entry
Database: PDB / ID: 1h0d
TitleCrystal structure of Human Angiogenin in complex with Fab fragment of its monoclonal antibody mAb 26-2F
Components
  • (ANTIBODY FAB FRAGMENT, ...) x 2
  • ANGIOGENIN
KeywordsIMMUNE SYSTEM/HYDROLASE / COMPLEX (ANTIBODY-HYDROLASE) / RIBONUCLEASE / ANTIBODY / IMMUNE SYSTEM-HYDROLASE complex
Function / homology
Function and homology information


angiogenin-PRI complex / tRNA-specific ribonuclease activity / negative regulation of translation in response to stress / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay / signaling / oocyte maturation / cell communication / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / homeostatic process ...angiogenin-PRI complex / tRNA-specific ribonuclease activity / negative regulation of translation in response to stress / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay / signaling / oocyte maturation / cell communication / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / homeostatic process / Adherens junctions interactions / hematopoietic stem cell proliferation / rRNA transcription / basement membrane / positive regulation of phosphorylation / RNA nuclease activity / ovarian follicle development / endocytic vesicle / actin filament polymerization / positive regulation of endothelial cell proliferation / peptide binding / RNA endonuclease activity / response to hormone / placenta development / positive regulation of protein secretion / stress granule assembly / negative regulation of smooth muscle cell proliferation / cytoplasmic stress granule / cell migration / heparin binding / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / growth cone / ribosome binding / endonuclease activity / actin binding / angiogenesis / response to hypoxia / defense response to Gram-positive bacterium / rRNA binding / copper ion binding / receptor ligand activity / signaling receptor binding / innate immune response / hydrolase activity / neuronal cell body / nucleolus / negative regulation of apoptotic process / signal transduction / protein homodimerization activity / DNA binding / : / extracellular region / nucleus / cytosol / cytoplasm
Similarity search - Function
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Roll ...P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Roll / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChavali, G.B. / Papageorgiou, A.C. / Acharya, K.R.
CitationJournal: Structure / Year: 2003
Title: The Crystal Structure of Human Angiogenin in Complex with an Antitumor Neutralizing Antibody
Authors: Chavali, G.B. / Papageorgiou, A.C. / Olson, K. / Fett, J. / Hu, G. / Shapiro, R. / Acharya, K.R.
History
DepositionJun 19, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 2.0Mar 11, 2020Group: Derived calculations / Polymer sequence / Category: entity_poly / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Dec 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANTIBODY FAB FRAGMENT, LIGHT CHAIN
B: ANTIBODY FAB FRAGMENT, HEAVY CHAIN
C: ANGIOGENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,71617
Polymers61,3953
Non-polymers1,32114
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7840 Å2
ΔGint-137.3 kcal/mol
Surface area25970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.580, 72.530, 86.990
Angle α, β, γ (deg.)90.00, 112.46, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-2019-

HOH

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Components

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Protein , 1 types, 1 molecules C

#3: Protein ANGIOGENIN / RIBONUCLEASE 5 / RNASE 5


Mass: 14152.006 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03950

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Antibody , 2 types, 2 molecules AB

#1: Antibody ANTIBODY FAB FRAGMENT, LIGHT CHAIN


Mass: 23584.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: HINGE REGION OBSERVED IN THE FAB FRAGMENT / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)
#2: Antibody ANTIBODY FAB FRAGMENT, HEAVY CHAIN


Mass: 23658.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: HINGE REGION OBSERVED IN THE FAB FRAGMENT / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)

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Non-polymers , 3 types, 341 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHERE ARE CHANGES IN RESIDUES FOR CHAIN A AND B (LYS146ARG,GLU165GL AND IN CHAIN B ARG189TRP) WITH ...THERE ARE CHANGES IN RESIDUES FOR CHAIN A AND B (LYS146ARG,GLU165GL AND IN CHAIN B ARG189TRP) WITH RESPECT TO THE KABAT DATABASE SEQUENCES FOR FAB CONSTANT REGION.
Has protein modificationY
Sequence detailsRESIDUES 128-133 OF CHAIN B WERE MODELLED AS GLYCINES. RESIDUES 198,199,210,211 OF CHAIN A WERE ...RESIDUES 128-133 OF CHAIN B WERE MODELLED AS GLYCINES. RESIDUES 198,199,210,211 OF CHAIN A WERE MODELLED AS ALANINES RESIDUES 134,213,214,215 OF CHAIN B WERE MODELLED AS ALANINES RESIDUES 1 OF CHAIN C WAS MODELLED AS ALANINE

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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: 2.86 Å3/Da / Density % sol: 57.04 %
Crystal growpH: 6 / Details: 30% PEG 3350 AND 0.2M LITHIUM SULPHATE PH 6.0-7.5
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails (eV)Chemical formula
130 %PEG80001reservoir
20.2 M1reservoirpH6.0-7.5Li2SO4
320 mg/mlprotein1droppH7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 46470 / % possible obs: 98.9 % / Redundancy: 3 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 17.6
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4.92 / % possible all: 97.8
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 40 Å / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
% possible obs: 97.8 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4.92

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1FVC,3HFL,1TET,1B1I

1fvc

3hfl
PDB Unreleased entry

1tet

1b1i


Resolution: 2→40 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1924 4.1 %RANDOM
Rwork0.232 ---
obs0.232 46469 98.9 %-
Displacement parametersBiso mean: 39.7 Å2
Baniso -1Baniso -2Baniso -3
1--12.65 Å20 Å2-4.23 Å2
2--24.85 Å20 Å2
3----12.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4290 0 76 327 4693
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.409 362 4.7 %
Rwork0.394 7286 -
obs--98.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4GLYCEROL.PARAMGLYCEROL.TOP
Refinement
*PLUS
Lowest resolution: 40 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.3

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