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- PDB-3q1s: HIV-1 neutralizing antibody Z13e1 in complex with epitope display... -

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Basic information

Entry
Database: PDB / ID: 3q1s
TitleHIV-1 neutralizing antibody Z13e1 in complex with epitope display protein
Components
  • Interleukin-22
  • Z13e1 Fab heavy chain
  • Z13e1 Fab light chain
KeywordsIMMUNE SYSTEM/CYTOKINE / immunoglobulin fold / antibody / gp41 / IMMUNE SYSTEM-CYTOKINE complex
Function / homology
Function and homology information


interleukin-22 receptor binding / Interleukin-20 family signaling / response to glucocorticoid / cytokine activity / acute-phase response / negative regulation of inflammatory response / Signaling by ALK fusions and activated point mutants / inflammatory response / extracellular space / extracellular region
Similarity search - Function
Interleukin-22 / Interleukin 22 IL-10-related T-cell-derived-inducible factor / Interleukin-10, conserved site / Interleukin-10 family signature. / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulins / Up-down Bundle / Immunoglobulin-like ...Interleukin-22 / Interleukin 22 IL-10-related T-cell-derived-inducible factor / Interleukin-10, conserved site / Interleukin-10 family signature. / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Interleukin-22
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsStanfield, R.L. / Julien, J.-P. / Pejchal, R. / Gach, J.S. / Zwick, M.B. / Wilson, I.A.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structure-Based Design of a Protein Immunogen that Displays an HIV-1 gp41 Neutralizing Epitope.
Authors: Stanfield, R.L. / Julien, J.P. / Pejchal, R. / Gach, J.S. / Zwick, M.B. / Wilson, I.A.
History
DepositionDec 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Sep 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Z13e1 Fab light chain
H: Z13e1 Fab heavy chain
I: Interleukin-22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,17615
Polymers65,1343
Non-polymers1,04112
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7870 Å2
ΔGint-31 kcal/mol
Surface area25960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.623, 99.216, 105.533
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules I

#3: Protein Interleukin-22 / IL-22 / Cytokine Zcyto18 / IL-10-related T-cell-derived-inducible factor / IL-TIF


Mass: 17370.980 Da / Num. of mol.: 1 / Fragment: UNP residues 29-179 / Mutation: S64W, L65N, A66W, N68D, N69I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL22, ILTIF, ZCYTO18, UNQ3099/PRO10096 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GZX6

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Antibody , 2 types, 2 molecules LH

#1: Antibody Z13e1 Fab light chain


Mass: 23096.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
#2: Antibody Z13e1 Fab heavy chain


Mass: 24666.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)

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Non-polymers , 3 types, 215 molecules

#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

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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: 45.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 19% PEG 4000, 10% isopropanol, 0.1M hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.058 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.058 Å / Relative weight: 1
ReflectionResolution: 2.15→49.63 Å / Num. all: 33242 / Num. obs: 33242 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rsym value: 0.117 / Net I/σ(I): 16

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0110refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3fn0

3fn0


Resolution: 2.15→49.63 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.915 / SU B: 12.738 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26024 1639 5 %RANDOM
Rwork0.2072 ---
obs0.20984 31381 99.84 %-
all-31381 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.892 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2---0.16 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.15→49.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4116 0 68 203 4387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224264
X-RAY DIFFRACTIONr_bond_other_d0.0010.022900
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.9745770
X-RAY DIFFRACTIONr_angle_other_deg1.07437082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4345526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45524.035171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.93815707
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7141523
X-RAY DIFFRACTIONr_chiral_restr0.0970.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214636
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02826
X-RAY DIFFRACTIONr_mcbond_it0.5741.52655
X-RAY DIFFRACTIONr_mcbond_other0.1761.51079
X-RAY DIFFRACTIONr_mcangle_it0.9924284
X-RAY DIFFRACTIONr_scbond_it1.69231609
X-RAY DIFFRACTIONr_scangle_it2.4514.51486
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 122 -
Rwork0.264 2273 -
obs-2395 100 %
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)
11.2918-0.7127-0.01554.24251.31153.8030.01990.0319-0.1268-0.01980.0464-0.18920.42880.0921-0.06630.08610.02740.01660.15830.00990.12341.82781.9729-6.3252
21.7156-0.3121-0.59983.5539-1.41493.6030.16180.17470.2552-0.3635-0.1376-0.1711-0.20270.0493-0.02410.31360.06850.06140.1963-0.02970.198710.84445.8006-41.1966
31.3645-0.3187-0.61212.2121-0.28583.2497-0.00990.09890.0126-0.21470.00930.0712-0.0282-0.12580.00060.02430.002-0.0070.119-0.01940.0972-7.41221.6848-7.8888
41.51060.41350.12597.93921.73133.9010.22450.2642-0.1337-0.5729-0.19940.67850.074-0.4394-0.02510.30710.0646-0.02820.3147-0.0270.2784-5.115710.5087-40.6243
55.4319-0.79816.79140.1462-0.99048.5309-0.3706-1.2029-0.11490.20820.28170.0978-0.6082-1.52170.08880.73820.05370.29320.6873-0.0690.49130.036320.928425.6427
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L3 - 107
2X-RAY DIFFRACTION2L108 - 211
3X-RAY DIFFRACTION3H1 - 123
4X-RAY DIFFRACTION4H124 - 137
5X-RAY DIFFRACTION4H143 - 195
6X-RAY DIFFRACTION4H205 - 225
7X-RAY DIFFRACTION5I40 - 46
8X-RAY DIFFRACTION5I58 - 102
9X-RAY DIFFRACTION5I119 - 179

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