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- PDB-3qeh: Crystal structure of human N12-i15, an ADCC and non-neutralizing ... -

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Basic information

Entry
Database: PDB / ID: 3qeh
TitleCrystal structure of human N12-i15, an ADCC and non-neutralizing anti-HIV-1 Env antibody
Components(Fab fragment of human anti-HIV-1 Env antibody N12- ...) x 2
KeywordsIMMUNE SYSTEM / ADCC and non-neutralizing anti-HIV-1 Env antibody N12-i15 / CD4i antibody / Fab fragment / binds to viral glycoprotein gp120
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsGuan, Y. / DeVico, A.L. / Lewis, G.K. / Pazgier, M.
CitationJournal: To be Published
Title: Crystal structure of human N12-i15, an ADCC and non-neutralizing anti-HIV-1 Env antibody
Authors: Guan, Y. / DeVico, A.L. / Lewis, G.K. / Pazgier, M.
History
DepositionJan 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type / 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 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab fragment of human anti-HIV-1 Env antibody N12-i15, heavy chain
B: Fab fragment of human anti-HIV-1 Env antibody N12-i15,light chain
C: Fab fragment of human anti-HIV-1 Env antibody N12-i15, heavy chain
D: Fab fragment of human anti-HIV-1 Env antibody N12-i15,light chain
E: Fab fragment of human anti-HIV-1 Env antibody N12-i15, heavy chain
F: Fab fragment of human anti-HIV-1 Env antibody N12-i15,light chain
G: Fab fragment of human anti-HIV-1 Env antibody N12-i15, heavy chain
H: Fab fragment of human anti-HIV-1 Env antibody N12-i15,light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,53025
Polymers195,5198
Non-polymers1,01117
Water10,196566
1
A: Fab fragment of human anti-HIV-1 Env antibody N12-i15, heavy chain
B: Fab fragment of human anti-HIV-1 Env antibody N12-i15,light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1187
Polymers48,8802
Non-polymers2385
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-68 kcal/mol
Surface area19610 Å2
MethodPISA
2
C: Fab fragment of human anti-HIV-1 Env antibody N12-i15, heavy chain
D: Fab fragment of human anti-HIV-1 Env antibody N12-i15,light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0786
Polymers48,8802
Non-polymers1984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-45 kcal/mol
Surface area19570 Å2
MethodPISA
3
E: Fab fragment of human anti-HIV-1 Env antibody N12-i15, heavy chain
F: Fab fragment of human anti-HIV-1 Env antibody N12-i15,light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1956
Polymers48,8802
Non-polymers3164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-46 kcal/mol
Surface area19820 Å2
MethodPISA
4
G: Fab fragment of human anti-HIV-1 Env antibody N12-i15, heavy chain
H: Fab fragment of human anti-HIV-1 Env antibody N12-i15,light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1396
Polymers48,8802
Non-polymers2594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-51 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.121, 125.121, 149.902
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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Antibody , 2 types, 8 molecules ACEGBDFH

#1: Antibody
Fab fragment of human anti-HIV-1 Env antibody N12-i15, heavy chain


Mass: 25036.100 Da / Num. of mol.: 4 / Fragment: Fab heavy chain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#2: Antibody
Fab fragment of human anti-HIV-1 Env antibody N12-i15,light chain


Mass: 23843.605 Da / Num. of mol.: 4 / Fragment: Fab light chain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Non-polymers , 4 types, 583 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 566 / 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: 3 Å3/Da / Density % sol: 59.01 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 01 M HEPES sodium, pH 7.5, 2% v/v PEG 400, 2 M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.979464 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979464 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.941
11K, H, -L20.059
ReflectionResolution: 2.59→50 Å / Num. all: 71684 / Num. obs: 71539 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.6 % / Rmerge(I) obs: 0.145 / Rsym value: 0.097 / Net I/σ(I): 16.3
Reflection shellResolution: 2.59→2.68 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.783 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.598 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.923 / Occupancy max: 1 / Occupancy min: 1 / SU B: 19.992 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25393 3615 5.1 %RANDOM
Rwork0.21602 ---
obs0.21797 67021 99.85 %-
all-67021 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.222 Å2
Baniso -1Baniso -2Baniso -3
1-4.57 Å20 Å20 Å2
2--4.57 Å20 Å2
3----9.13 Å2
Refinement stepCycle: LAST / Resolution: 2.59→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12831 0 49 566 13446
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02213158
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7721.95117866
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.47251641
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.71824.067541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.458152112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.6921563
X-RAY DIFFRACTIONr_chiral_restr0.1150.22021
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0219835
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7651.58288
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.487213422
X-RAY DIFFRACTIONr_scbond_it2.47934870
X-RAY DIFFRACTIONr_scangle_it4.0634.54444
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.599→2.665 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.559 267 -
Rwork0.462 4761 -
obs--98.01 %
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)
11.312-1.4492-0.00582.9475-0.0240.73020.031-0.0280.04130.1712-0.02880.1204-0.1029-0.0203-0.00220.1135-0.0570.02430.0793-0.00820.014457.1038-37.3552-8.7296
20.7482-1.2606-0.45673.25261.50141.26670.17640.15590.0503-0.2869-0.30980.218-0.2887-0.11930.13340.18550.0192-0.00220.080.00290.076352.522-29.3884-24.8627
32.5578-0.7844-0.55930.99290.19780.92820.18150.11710.0501-0.0713-0.09470.14680.035-0.2394-0.08680.1079-0.07180.00860.1732-0.00230.032137.1624-61.2534-0.5766
43.3585-1.18960.80640.8234-0.24030.70120.0016-0.23040.04440.02690.02650.19280.1013-0.2818-0.02810.0625-0.07770.01280.3031-0.02250.106628.6508-57.717315.9772
51.40350.7717-0.10231.6866-0.17641.77640.0434-0.1478-0.03770.10890.0692-0.2064-0.0360.4347-0.11260.09260.0636-0.02410.257-0.07180.028524.25865.568536.8775
62.32980.99860.66041.33960.00841.6121-0.1180.07270.054-0.08450.1274-0.27490.01250.6425-0.00940.03840.00160.01260.4398-0.10690.103232.116410.617620.6815
71.24090.95390.03822.3245-0.59971.21860.07870.1541-0.1702-0.12670.0893-0.16850.62860.246-0.1680.45670.16-0.06790.1492-0.05370.0519-0.1285-24.5262-28.9627
80.96541.15450.552.45930.76060.80940.2617-0.1383-0.27290.2257-0.1052-0.01250.69790.1458-0.15650.8660.0807-0.09720.20480.01220.1994-6.1659-32.5219-12.2413
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 212
2X-RAY DIFFRACTION2B1 - 210
3X-RAY DIFFRACTION3C1 - 212
4X-RAY DIFFRACTION4D1 - 210
5X-RAY DIFFRACTION5E1 - 212
6X-RAY DIFFRACTION6F1 - 210
7X-RAY DIFFRACTION7G1 - 201
8X-RAY DIFFRACTION8H2 - 210

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