PDB-3q6f: Crystal structure of Fab of human mAb 2909 specific for quaternar...

Basic information

• Entry: Database: PDB / ID: 3q6f
• Title: Crystal structure of Fab of human mAb 2909 specific for quaternary neutralizing epitope of HIV-1 gp120

Components

• Heavy chain of Fab of human mAb 2909
• Light chain of Fab of human mAb 2909

• Keywords: IMMUNE SYSTEM / IgG / neutralization of HIV-1 viruses / Quaternary epitope of HIV-1 gp120
• Function / homology: Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DI(HYDROXYETHYL)ETHER
• Biological species: Homo sapiens (human)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.192 Å
• Authors: Spurrier, B. / Sampson, J. / Totrov, M. / Li, H. / O'Neal, T. / William, C. / Robinson, J. / Gorny, M.K. / Zolla-Pazner, S. / Kong, X.P.
• Citation: Journal: Structure / Year: 2011; Title: Structural Analysis of Human and Macaque mAbs 2909 and 2.5B: Implications for the Configuration of the Quaternary Neutralizing Epitope of HIV-1 gp120.; Authors: Spurrier, B. / Sampson, J.M. / Totrov, M. / Li, H. / O'Neal, T. / Williams, C. / Robinson, J. / Gorny, M.K. / Zolla-Pazner, S. / Kong, X.P.

History

Deposition	Dec 31, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 25, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 12, 2011	Group: Derived calculations

Assembly

Deposited unit

A: Light chain of Fab of human mAb 2909

B: Heavy chain of Fab of human mAb 2909

C: Light chain of Fab of human mAb 2909

D: Heavy chain of Fab of human mAb 2909

E: Light chain of Fab of human mAb 2909

F: Heavy chain of Fab of human mAb 2909

G: Light chain of Fab of human mAb 2909

H: Heavy chain of Fab of human mAb 2909

I: Light chain of Fab of human mAb 2909

J: Heavy chain of Fab of human mAb 2909

K: Light chain of Fab of human mAb 2909

L: Heavy chain of Fab of human mAb 2909

hetero molecules

Summary:

• 289 kDa, 12 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	288,896	18
Polymers	288,259	12
Non-polymers	637	6
Water	0	0

1

A: Light chain of Fab of human mAb 2909

B: Heavy chain of Fab of human mAb 2909

hetero molecules

Summary:

• defined by author&software
• 48.1 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	48,149	3
Polymers	48,043	2
Non-polymers	106	1
Water	0

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	3880 Å2
ΔGint	-24 kcal/mol
Surface area	20510 Å2
Method	PISA

2

C: Light chain of Fab of human mAb 2909

D: Heavy chain of Fab of human mAb 2909

hetero molecules

Summary:

• defined by author&software
• 48.1 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	48,149	3
Polymers	48,043	2
Non-polymers	106	1
Water	0

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	3740 Å2
ΔGint	-24 kcal/mol
Surface area	20580 Å2
Method	PISA

3

E: Light chain of Fab of human mAb 2909

F: Heavy chain of Fab of human mAb 2909

hetero molecules

Summary:

• defined by author&software
• 48.1 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	48,149	3
Polymers	48,043	2
Non-polymers	106	1
Water	0

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	3850 Å2
ΔGint	-24 kcal/mol
Surface area	20710 Å2
Method	PISA

4

G: Light chain of Fab of human mAb 2909

H: Heavy chain of Fab of human mAb 2909

hetero molecules

Summary:

• defined by author&software
• 48.1 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	48,149	3
Polymers	48,043	2
Non-polymers	106	1
Water	0

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	3860 Å2
ΔGint	-24 kcal/mol
Surface area	20470 Å2
Method	PISA

5

I: Light chain of Fab of human mAb 2909

J: Heavy chain of Fab of human mAb 2909

hetero molecules

Summary:

• defined by author&software
• 48.1 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	48,149	3
Polymers	48,043	2
Non-polymers	106	1
Water	0

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	3850 Å2
ΔGint	-21 kcal/mol
Surface area	20660 Å2
Method	PISA

6

K: Light chain of Fab of human mAb 2909

L: Heavy chain of Fab of human mAb 2909

hetero molecules

Summary:

• defined by author&software
• 48.1 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	48,149	3
Polymers	48,043	2
Non-polymers	106	1
Water	0

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	3780 Å2
ΔGint	-22 kcal/mol
Surface area	20560 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	178.504, 178.504, 218.900
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3221

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1
4	1
5	1
6	1
1	2
2	2
3	2
4	2
5	2
6	2
1	3
2	3
3	3
4	3
5	3
6	3
1	4
2	4
3	4
4	4
5	4
6	4
1	5
2	5
3	5
4	5
5	5
6	5

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	chain A and (resid 3:106a)
2	1	1	chain C and (resid 3:106a)
3	1	1	chain E and (resid 3:106a)
4	1	1	chain G and (resid 3:106a)
5	1	1	chain I and (resid 3:106a)
6	1	1	chain K and (resid 3:106a)
1	1	2	chain A and (resid 107:153 or resid 159:165 or resid 171:207)
2	1	2	chain C and (resid 107:153 or resid 159:165 or resid 171:207)
3	1	2	chain E and (resid 107:153 or resid 159:165 or resid 171:207)
4	1	2	chain G and (resid 107:153 or resid 159:165 or resid 171:207)
5	1	2	chain I and (resid 107:153 or resid 159:165 or resid 171:207)
6	1	2	chain K and (resid 107:153 or resid 159:165 or resid 171:207)
1	1	3	chain B and (resid 2:97 or resid 100k:113)
2	1	3	chain D and (resid 2:97 or resid 100k:113)
3	1	3	chain F and (resid 2:97 or resid 100k:113)
4	1	3	chain H and (resid 2:97 or resid 100k:113)
5	1	3	chain J and (resid 2:97 or resid 100k:113)
6	1	3	chain L and (resid 2:97 or resid 100k:113)
1	1	4	chain B and (resid 114:126 or resid 135:213)
2	1	4	chain D and (resid 114:126 or resid 135:213)
3	1	4	chain F and (resid 114:126 or resid 135:213)
4	1	4	chain H and (resid 114:126 or resid 135:213)
5	1	4	chain J and (resid 114:126 or resid 135:213)
6	1	4	chain L and (resid 114:126 or resid 135:213)
1	1	5	chain B and (resid 98:100j) and backbone
2	1	5	chain D and (resid 98:100j) and backbone
3	1	5	chain F and (resid 98:100j) and backbone
4	1	5	chain H and (resid 98:100j) and backbone
5	1	5	chain J and (resid 98:100j) and backbone
6	1	5	chain L and (resid 98:100j) and backbone

NCS ensembles :

ID
1
2
3
4
5

Components

#1: Antibody

A C E G I K
Light chain of Fab of human mAb 2909

Details:

Mass: 22813.189 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

#2: Antibody

B D F H J L
Heavy chain of Fab of human mAb 2909

Details:

Mass: 25230.004 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

#3: Chemical

A-212 C-212 E-212 G-212 I-212 K-212
ChemComp-PEG / DI(HYDROXYETHYL)ETHER

Details:

Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₄H₁₀O₃

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

• Crystal: Density Matthews: 3.5 ų/Da / Density % sol: 64.9 %
• Crystal grow: Temperature: 296 K / Method: evaporation / pH: 6.8 ; Details: 14% PEG 8000, 0.1M HEPES, pH6.8, 0.1M glycine, and 8% ethylene glycol, under the oil, temperature 296K, EVAPORATION

Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1
3		1
4		1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	APS	23-ID-B	1	1.03321
SYNCHROTRON	NSLS	X6A	2	1
SYNCHROTRON	APS	17-ID	3	1
SYNCHROTRON	NSLS	X4C	4	1

Detector

Type	ID	Detector	Date
MAR scanner 300 mm plate	1	IMAGE PLATE	Feb 18, 2010
	2
	3
	4

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	MIRRORS	SINGLE WAVELENGTH	M	x-ray	1
2				x-ray	1
3				x-ray	1
4				x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.03321	1
2	1	1

• Reflection: Resolution: 3→50 Å / Num. obs: 66903 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
• Reflection shell: Resolution: 3→3.05 Å / % possible all: 78.3

Processing

Software

Name	Version	Classification
Blu-Ice		data collection
MOLREP		phasing
PHENIX	(phenix.refine: 1.6.4_486)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.192→46.653 Å / SU ML: 0.39 / σ(F): 0.19 / Phase error: 24.54 / Stereochemistry target values: ML

	Rfactor	Num. reflection	% reflection
Rfree	0.2429	3391	5.07 %
Rwork	0.199	-	-
obs	0.2013	66876	99.25 %
all	-	66903	-

• Solvent computation: Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 43.061 Ų / k_sol: 0.277 e/ų

Displacement parameters

	Baniso -1	Baniso -2	Baniso -3
1-	-2.7791 Å2	-0 Å2	0 Å2
2-	-	-2.7791 Å2	-0 Å2
3-	-	-	5.5582 Å2

Refinement step

Cycle: LAST / Resolution: 3.192→46.653 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20042	0	42	0	20084

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	20618
X-RAY DIFFRACTION	f_angle_d	1.234	28074
X-RAY DIFFRACTION	f_dihedral_angle_d	15.868	7276
X-RAY DIFFRACTION	f_chiral_restr	0.079	3097
X-RAY DIFFRACTION	f_plane_restr	0.005	3603

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	800	X-RAY DIFFRACTION	POSITIONAL
1	2	C	800	X-RAY DIFFRACTION	POSITIONAL	0.048
1	3	E	800	X-RAY DIFFRACTION	POSITIONAL	0.042
1	4	G	800	X-RAY DIFFRACTION	POSITIONAL	0.047
1	5	I	800	X-RAY DIFFRACTION	POSITIONAL	0.06
1	6	K	800	X-RAY DIFFRACTION	POSITIONAL	0.042
2	1	A	686	X-RAY DIFFRACTION	POSITIONAL
2	2	C	686	X-RAY DIFFRACTION	POSITIONAL	0.055
2	3	E	686	X-RAY DIFFRACTION	POSITIONAL	0.051
2	4	G	686	X-RAY DIFFRACTION	POSITIONAL	0.075
2	5	I	686	X-RAY DIFFRACTION	POSITIONAL	0.06
2	6	K	686	X-RAY DIFFRACTION	POSITIONAL	0.076
3	1	B	865	X-RAY DIFFRACTION	POSITIONAL
3	2	D	865	X-RAY DIFFRACTION	POSITIONAL	0.05
3	3	F	865	X-RAY DIFFRACTION	POSITIONAL	0.049
3	4	H	865	X-RAY DIFFRACTION	POSITIONAL	0.056
3	5	J	865	X-RAY DIFFRACTION	POSITIONAL	0.066
3	6	L	865	X-RAY DIFFRACTION	POSITIONAL	0.05
4	1	B	673	X-RAY DIFFRACTION	POSITIONAL
4	2	D	673	X-RAY DIFFRACTION	POSITIONAL	0.048
4	3	F	673	X-RAY DIFFRACTION	POSITIONAL	0.044
4	4	H	673	X-RAY DIFFRACTION	POSITIONAL	0.054
4	5	J	673	X-RAY DIFFRACTION	POSITIONAL	0.057
4	6	L	673	X-RAY DIFFRACTION	POSITIONAL	0.045
5	1	B	64	X-RAY DIFFRACTION	POSITIONAL
5	2	D	64	X-RAY DIFFRACTION	POSITIONAL	0.079
5	3	F	64	X-RAY DIFFRACTION	POSITIONAL	0.052
5	4	H	64	X-RAY DIFFRACTION	POSITIONAL	0.087
5	5	J	64	X-RAY DIFFRACTION	POSITIONAL	0.087
5	6	L	64	X-RAY DIFFRACTION	POSITIONAL	0.066

LS refinement shell

Resolution (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	Refine-ID	% reflection obs (%)
3.192-3.306	0.3551	323	0.3305	6030	X-RAY DIFFRACTION	96
3.306-3.4384	0.3248	347	0.2869	6307	X-RAY DIFFRACTION	100
3.4384-3.5948	0.3154	332	0.2646	6309	X-RAY DIFFRACTION	100
3.5948-3.7843	0.2754	316	0.236	6361	X-RAY DIFFRACTION	100
3.7843-4.0212	0.2785	339	0.2194	6325	X-RAY DIFFRACTION	100
4.0212-4.3315	0.2352	342	0.1881	6338	X-RAY DIFFRACTION	100
4.3315-4.767	0.2192	347	0.162	6359	X-RAY DIFFRACTION	100
4.767-5.4559	0.1808	318	0.1504	6431	X-RAY DIFFRACTION	100
5.4559-6.8703	0.2164	371	0.1713	6434	X-RAY DIFFRACTION	100
6.8703-46.6584	0.2272	356	0.1873	6591	X-RAY DIFFRACTION	99