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- PDB-3piq: Crystal structure of human 2909 Fab, a quaternary structure-speci... -

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Entry
Database: PDB / ID: 3piq
TitleCrystal structure of human 2909 Fab, a quaternary structure-specific antibody against HIV-1
Components
  • Human monoclonal antibody 2909 Fab heavy chain
  • Human monoclonal antibody 2909 Fab light chain
KeywordsIMMUNE SYSTEM / monoclonal antibody / neutralizing / HIV-1 / quaternary epitope / trimeric envelope spike
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.325 Å
AuthorsChangela, A. / Gorny, M.K. / Zolla-Pazner, S. / Kwong, P.D.
CitationJournal: J.Virol. / Year: 2011
Title: Crystal Structure of Human Antibody 2909 Reveals Conserved Features of Quaternary Structure-Specific Antibodies That Potently Neutralize HIV-1.
Authors: Changela, A. / Wu, X. / Yang, Y. / Zhang, B. / Zhu, J. / Nardone, G.A. / O'Dell, S. / Pancera, M. / Gorny, M.K. / Phogat, S. / Robinson, J.E. / Stamatatos, L. / Zolla-Pazner, S. / Mascola, J.R. / Kwong, P.D.
History
DepositionNov 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Human monoclonal antibody 2909 Fab heavy chain
L: Human monoclonal antibody 2909 Fab light chain
A: Human monoclonal antibody 2909 Fab heavy chain
B: Human monoclonal antibody 2909 Fab light chain
C: Human monoclonal antibody 2909 Fab heavy chain
D: Human monoclonal antibody 2909 Fab light chain
E: Human monoclonal antibody 2909 Fab heavy chain
F: Human monoclonal antibody 2909 Fab light chain
G: Human monoclonal antibody 2909 Fab heavy chain
I: Human monoclonal antibody 2909 Fab light chain
J: Human monoclonal antibody 2909 Fab heavy chain
K: Human monoclonal antibody 2909 Fab light chain


Theoretical massNumber of molelcules
Total (without water)284,94312
Polymers284,94312
Non-polymers00
Water00
1
H: Human monoclonal antibody 2909 Fab heavy chain
L: Human monoclonal antibody 2909 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,4912
Polymers47,4912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-26 kcal/mol
Surface area20990 Å2
MethodPISA
2
A: Human monoclonal antibody 2909 Fab heavy chain
B: Human monoclonal antibody 2909 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,4912
Polymers47,4912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-23 kcal/mol
Surface area20240 Å2
MethodPISA
3
C: Human monoclonal antibody 2909 Fab heavy chain
D: Human monoclonal antibody 2909 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,4912
Polymers47,4912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-24 kcal/mol
Surface area20930 Å2
MethodPISA
4
E: Human monoclonal antibody 2909 Fab heavy chain
F: Human monoclonal antibody 2909 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,4912
Polymers47,4912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-24 kcal/mol
Surface area20150 Å2
MethodPISA
5
G: Human monoclonal antibody 2909 Fab heavy chain
I: Human monoclonal antibody 2909 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,4912
Polymers47,4912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-24 kcal/mol
Surface area20900 Å2
MethodPISA
6
J: Human monoclonal antibody 2909 Fab heavy chain
K: Human monoclonal antibody 2909 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,4912
Polymers47,4912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-23 kcal/mol
Surface area21060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.373, 180.373, 222.526
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Antibody
Human monoclonal antibody 2909 Fab heavy chain


Mass: 24907.670 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)
#2: Antibody
Human monoclonal antibody 2909 Fab light chain


Mass: 22582.885 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)
Sequence detailsTHE NATIVE N-TERMINAL SERINE IN THE 2909 LIGHT CHAIN IS MISSING DUE TO ALTERATION OF THE SIGNAL ...THE NATIVE N-TERMINAL SERINE IN THE 2909 LIGHT CHAIN IS MISSING DUE TO ALTERATION OF THE SIGNAL PEPTIDE SEQUENCE IN THE IMMUNOGLOBULIN EXPRESSED BY TRANSIENT TRANSFECTION FROM SYNTHETIC GENE.

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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: 3.67 Å3/Da / Density % sol: 66.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 17% PEG 8000, 0.1M Tris-Cl (pH 8.5), 0.1M NaCl, 3% galactose, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.325→50 Å / Num. obs: 49978 / % possible obs: 81.5 % / Observed criterion σ(I): 1 / Redundancy: 5.1 % / Rsym value: 0.156 / Net I/σ(I): 8.8
Reflection shellResolution: 3.325→3.36 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.95 / Num. unique all: 1322 / Rsym value: 0.449 / % possible all: 43.6

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3LRS

3lrs


Resolution: 3.325→22.375 Å / SU ML: 0.45 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2991 2452 5.12 %RANDOM
Rwork0.2365 ---
obs0.2397 47907 77.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.166 Å2 / ksol: 0.267 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--25.0592 Å20 Å20 Å2
2---25.0592 Å20 Å2
3---50.1185 Å2
Refinement stepCycle: LAST / Resolution: 3.325→22.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19449 0 0 0 19449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00319971
X-RAY DIFFRACTIONf_angle_d0.57727218
X-RAY DIFFRACTIONf_dihedral_angle_d9.8637032
X-RAY DIFFRACTIONf_chiral_restr0.043031
X-RAY DIFFRACTIONf_plane_restr0.0033506
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
3.325-3.38910.3698380.343678282024
3.3891-3.45810.4289550.32171376143142
3.4581-3.5330.3463890.3221544163348
3.533-3.61480.38081080.32751678178653
3.6148-3.70480.38851070.30731875198259
3.7048-3.80450.35761060.30262107221365
3.8045-3.91590.35931110.28282337244871
3.9159-4.04160.35911270.28412557268479
4.0416-4.18510.31671490.25722734288384
4.1851-4.35150.25291630.22032906306990
4.3515-4.5480.30141850.19652987317293
4.548-4.78560.27881720.19543085325795
4.7856-5.08210.22691780.19273108328696
5.0821-5.46920.29031610.19343178333997
5.4692-6.00990.3051640.22533230339498
6.0099-6.85760.32961750.22913273344899
6.8576-8.55860.26331840.22713292347699
8.5586-22.37540.25941800.22783406358699
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)
10.95110.40120.6651.70890.39170.77440.1271-0.0132-0.0863-0.00680.18820.11310.1518-0.2672-0.30050.5379-0.0762-0.3570.4904-0.06950.9967-91.63-0.789355.7289
22.304-2.63441.222.8218-1.01980.9234-0.32580.0625-0.28690.2054-0.0246-0.6402-0.21480.00180.34720.8142-0.0096-0.55070.5467-0.13061.225-55.905-7.50565.0506
31.49850.6842-0.39150.78130.10111.8213-0.4603-0.00840.7489-0.04160.46710.2596-0.0901-0.41080.11350.4687-0.0091-0.42240.5490.00960.8104-83.283720.145258.1717
41.05490.1799-1.06660.08470.39513.68-0.3408-0.1676-1.0813-0.1246-0.3287-0.40250.41260.21610.81430.6329-0.0234-0.15540.1553-0.04791.2602-52.11244.394252.9481
51.3513-1.7504-0.1422.4274-0.3241.13130.0438-0.21880.4893-0.24030.1307-0.54880.0362-0.0171-0.23220.3385-0.1139-0.03050.3967-0.08020.954438.1931-60.685253.7089
64.83130.0313-2.65134.16750.7371.51720.3194-2.13770.9087-0.29360.0139-1.2563-0.2125-0.2574-0.34290.5144-0.14250.06651.4889-0.49021.012725.5246-24.783161.8871
70.8241-0.4119-0.89071.14910.6190.6471-0.06220.5370.22630.10990.30480.9257-0.1501-0.2818-0.25640.4809-0.0674-0.12260.69080.090.925915.9861-62.016454.9104
81.21120.4332-1.65093.2672-0.83262.2141-0.314-0.2251.32240.05641.11661.5389-0.3131-0.3401-0.74460.4432-0.2416-0.26780.60510.14131.048714.8394-26.851948.7462
92.03420.1396-0.6541.3868-0.52990.27240.05670.29510.1199-0.24650.18430.16930.40040.12960.04090.61760.1371-0.01170.3596-0.16330.085623.7305-82.733920.0331
102.558-1.47840.7043.4088-2.74691.99460.28080.1557-0.2570.4404-0.07720.3566-0.21710.1824-0.26630.39730.0008-0.020.2205-0.10720.43420.3501-54.426812.8462
112.10.84250.3411.2058-0.57031.12590.5666-0.05070.4818-0.1597-0.26120.15470.02580.54-0.31440.30960.05870.02360.5734-0.24570.746137.6114-64.705919.0698
121.0489-0.4209-0.61850.7176-0.47650.7754-0.0874-0.0155-0.2951-0.3086-0.1634-0.4298-0.45810.05380.23070.3191-0.0456-0.02010.2712-0.20520.43248.2002-46.434425.5858
132.16-1.4831-1.12391.5668-0.06951.2744-0.0402-0.63290.2531-0.0653-0.20060.01390.33450.05850.00620.394-0.0102-0.14380.52160.14121.1069-17.4652-36.61853.8978
146.91390.0252-1.71666.8871-2.58291.83790.2744-0.37531.88392.39930.1904-0.46490.44830.1546-0.40181.3041-0.1569-0.15450.24380.00730.5235-55.4887-29.491663.4358
151.82850.54660.07610.208-0.26221.458-0.286-0.2849-0.13370.05010.1466-0.11240.80790.06640.23760.68130.1417-0.00250.48090.09780.8625-27.5443-56.239855.2529
160.22440.9797-0.19782.9737-0.74571.4702-0.36270.12820.4371-0.80280.35960.90960.04330.0844-0.11070.8082-0.1769-0.1930.29890.17980.8101-57.8547-39.917550.2496
172.93760.60410.68210.3970.74072.07610.83860.1472-0.7020.2380.1418-0.57880.4764-0.0152-1.03880.537-0.0395-0.50340.3712-0.03781.3343-36.7722-16.459894.3403
1810.05060.78474.13381.20360.96136.0682-2.0861.38272.54310.17040.66580.7154-0.44060.28851.39660.8246-0.3847-0.71210.81940.34371.387-10.3462-45.595585.4759
190.8845-0.7317-0.77731.11730.06720.99360.74090.0799-0.8946-0.1418-0.24-1.05870.3633-0.1436-0.70040.8609-0.197-0.58360.43960.05471.3376-48.6168-35.2192.8967
206.8883.60616.34642.69172.16426.8913-0.3298-1.36341.7876-0.3409-1.15180.42530.6336-1.25911.28390.6549-0.2971-0.2830.83310.04161.0507-19.1173-53.475297.9551
213.37570.28010.79472.41651.72991.1665-0.41720.31120.08330.33560.30510.1104-0.29710.0114-0.14030.28420.0760.11470.15090.02760.1104-43.9684-36.501117.8604
222.0984-1.20610.69034.60274.27324.85120.1088-0.2522-0.12040.1138-0.023-1.53230.46920.0295-0.29110.4276-0.04530.14550.1183-0.20710.624-18.5354-65.763612.5426
234.9541.41.09431.18452.03013.7260.30070.7083-1.15810.31560.42640.14320.580.03180.35310.15250.03920.24660.12440.26060.0646-56.0262-54.77816.769
241.03110.59090.94060.34170.61790.5614-0.02260.0342-0.2852-0.1597-0.2495-0.05520.02390.05540.26980.4039-0.03940.0330.46450.14710.5221-26.881-73.475825.147
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 1:113)
2X-RAY DIFFRACTION2chain A and (resid 114:214)
3X-RAY DIFFRACTION3chain B and (resid 2:110)
4X-RAY DIFFRACTION4chain B and (resid 111:208)
5X-RAY DIFFRACTION5chain C and (resid 1:113)
6X-RAY DIFFRACTION6chain C and (resid 114:214)
7X-RAY DIFFRACTION7chain D and (resid 2:110)
8X-RAY DIFFRACTION8chain D and (resid 111:208)
9X-RAY DIFFRACTION9chain E and (resid 1:113)
10X-RAY DIFFRACTION10chain E and (resid 114:214)
11X-RAY DIFFRACTION11chain F and (resid 2:110)
12X-RAY DIFFRACTION12chain F and (resid 111:208)
13X-RAY DIFFRACTION13chain G and (resid 1:113)
14X-RAY DIFFRACTION14chain G and (resid 114:214)
15X-RAY DIFFRACTION15chain I and (resid 2:110)
16X-RAY DIFFRACTION16chain I and (resid 111:208)
17X-RAY DIFFRACTION17chain J and (resid 1:113)
18X-RAY DIFFRACTION18chain J and (resid 114:214)
19X-RAY DIFFRACTION19chain K and (resid 2:110)
20X-RAY DIFFRACTION20chain K and (resid 111:208)
21X-RAY DIFFRACTION21chain H and (resid 1:113)
22X-RAY DIFFRACTION22chain H and (resid 114:214)
23X-RAY DIFFRACTION23chain L and (resid 2:110)
24X-RAY DIFFRACTION24chain L and (resid 111:208)

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