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- PDB-3tnn: Crystal structure of N5-i5 Fab, an ADCC mediating and non-neutral... -

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Basic information

Entry
Database: PDB / ID: 3tnn
TitleCrystal structure of N5-i5 Fab, an ADCC mediating and non-neutralizing CD4i anti-HIV- 1 antibody.
Components
  • Fab heavy chain of ADCC and non-neutralizing anti-HIV-1 antibody N5-i5
  • Fab light chain of ADCC and non-neutralizing anti-HIV-1 antibody N5-i5
KeywordsIMMUNE SYSTEM / ANTI-HIV-1 ENV ANTIBODY n5-i5 / CD4i antibody / ADCC / HIV-1 Env
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWu, X. / Pazgier, M.
CitationJournal: To be Published
Title: Crystal structure of N5-i5 Fab, an ADCC and non-neutralizing anti-HIV-1 antibody
Authors: Guan, J. / Wu, X. / Pazgier, M. / Lewis, G.
History
DepositionSep 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Derived calculations / Source and taxonomy / Category: entity_src_gen / struct_site
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name ..._entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab heavy chain of ADCC and non-neutralizing anti-HIV-1 antibody N5-i5
L: Fab light chain of ADCC and non-neutralizing anti-HIV-1 antibody N5-i5
A: Fab heavy chain of ADCC and non-neutralizing anti-HIV-1 antibody N5-i5
B: Fab light chain of ADCC and non-neutralizing anti-HIV-1 antibody N5-i5
C: Fab heavy chain of ADCC and non-neutralizing anti-HIV-1 antibody N5-i5
D: Fab light chain of ADCC and non-neutralizing anti-HIV-1 antibody N5-i5
E: Fab heavy chain of ADCC and non-neutralizing anti-HIV-1 antibody N5-i5
F: Fab light chain of ADCC and non-neutralizing anti-HIV-1 antibody N5-i5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,38032
Polymers186,9318
Non-polymers1,44924
Water14,448802
1
H: Fab heavy chain of ADCC and non-neutralizing anti-HIV-1 antibody N5-i5
L: Fab light chain of ADCC and non-neutralizing anti-HIV-1 antibody N5-i5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,34711
Polymers46,7332
Non-polymers6149
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-21 kcal/mol
Surface area18860 Å2
MethodPISA
2
A: Fab heavy chain of ADCC and non-neutralizing anti-HIV-1 antibody N5-i5
B: Fab light chain of ADCC and non-neutralizing anti-HIV-1 antibody N5-i5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9356
Polymers46,7332
Non-polymers2024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-23 kcal/mol
Surface area18870 Å2
MethodPISA
3
C: Fab heavy chain of ADCC and non-neutralizing anti-HIV-1 antibody N5-i5
D: Fab light chain of ADCC and non-neutralizing anti-HIV-1 antibody N5-i5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9966
Polymers46,7332
Non-polymers2634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-25 kcal/mol
Surface area18760 Å2
MethodPISA
4
E: Fab heavy chain of ADCC and non-neutralizing anti-HIV-1 antibody N5-i5
F: Fab light chain of ADCC and non-neutralizing anti-HIV-1 antibody N5-i5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1029
Polymers46,7332
Non-polymers3697
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-24 kcal/mol
Surface area18730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.437, 84.505, 143.125
Angle α, β, γ (deg.)90.00, 101.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 8 molecules HACELBDF

#1: Antibody
Fab heavy chain of ADCC and non-neutralizing anti-HIV-1 antibody N5-i5


Mass: 23789.602 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#2: Antibody
Fab light chain of ADCC and non-neutralizing anti-HIV-1 antibody N5-i5


Mass: 22943.248 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 826 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 802 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium Sulfate, 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 123808 / Num. obs: 115389 / % possible obs: 93.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.113 / Rsym value: 0.082 / Net I/σ(I): 12.7
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.765 / Mean I/σ(I) obs: 2 / Rsym value: 0.613 / % possible all: 98.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / SU B: 10.587 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24482 6188 5 %RANDOM
Rwork0.19786 ---
all0.2 117330 --
obs0.20019 -97.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.312 Å2
Baniso -1Baniso -2Baniso -3
1-3.84 Å20 Å21.28 Å2
2---2.56 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12561 0 66 802 13429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02212901
X-RAY DIFFRACTIONr_angle_refined_deg1.7411.95617570
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.30351677
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.19924.039463
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.174151974
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.391552
X-RAY DIFFRACTIONr_chiral_restr0.1290.21993
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0219652
X-RAY DIFFRACTIONr_mcbond_it1.1061.58391
X-RAY DIFFRACTIONr_mcangle_it1.935213530
X-RAY DIFFRACTIONr_scbond_it3.03934510
X-RAY DIFFRACTIONr_scangle_it4.7734.54040
LS refinement shellResolution: 1.944→1.994 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 410 -
Rwork0.279 7724 -
obs--88.27 %
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)
10.2892-0.082-0.13350.02410.02290.5196-0.02450.0102-0.00990.0108-0.0024-0.0026-0.0356-0.0050.02690.02170.0055-0.04140.1242-0.00020.149327.919349.612215.7269
20.03220.0481-0.10520.2824-0.27860.49640.02110.02610.0030.09810.0095-0.0247-0.08410.0093-0.03070.0616-0.0107-0.02570.1272-0.00470.117934.322565.24822.7566
30.0119-0.01690.04910.3835-0.10660.8131-0.01150.0288-0.01360.12090.02090.0676-0.1432-0.0601-0.00940.08750.01730.01610.1331-0.02610.090919.230424.204851.6113
40.020.02-0.14060.139-0.29161.8558-0.0120.01180.01760.0263-0.0110.02050.110.07570.0230.10240.010.02770.1007-0.00480.087129.059.740148.1163
50.0810.1331-0.07260.5720.4511.06710.01410.00940.01750.0435-0.06430.0909-0.0343-0.05370.05020.10320.04320.05720.0985-0.00730.087556.51673.990451.565
60.04170.0858-0.15240.3042-0.26011.4081-0.01970.0220.00690.0687-0.0277-0.00210.0964-0.00070.04750.13620.02520.01340.10470.01510.071565.7399-10.995447.8814
70.1207-0.0025-0.12170.0033-0.01680.518-0.01470.00770.00080.00480.01170.0032-0.0191-0.01240.0030.02910.0049-0.04730.12890.00460.147364.457928.547615.6435
80.05730.0775-0.11630.141-0.16460.40110.03460.03380.01150.08690.0052-0.0035-0.04170.0266-0.03980.0755-0.0084-0.02770.1191-0.00480.121470.877344.444722.4067
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 212
2X-RAY DIFFRACTION2L4 - 210
3X-RAY DIFFRACTION3A1 - 213
4X-RAY DIFFRACTION4B4 - 210
5X-RAY DIFFRACTION5C1 - 213
6X-RAY DIFFRACTION6D4 - 210
7X-RAY DIFFRACTION7E1 - 211
8X-RAY DIFFRACTION8F4 - 210

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